From 95ef11e9cde59dc9894b6b0af03a0b9701439d8e Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Thu, 19 Jun 2025 08:02:57 -0700
Subject: [PATCH 01/52] build: allow quick iteration on meta.yaml

---
 .github/actions/curl-meta-yaml/action.yaml | 30 +++++++++++++++++-----
 1 file changed, 24 insertions(+), 6 deletions(-)

diff --git a/.github/actions/curl-meta-yaml/action.yaml b/.github/actions/curl-meta-yaml/action.yaml
index 16bda7ab..63a757ee 100644
--- a/.github/actions/curl-meta-yaml/action.yaml
+++ b/.github/actions/curl-meta-yaml/action.yaml
@@ -5,21 +5,39 @@ runs:
   steps:
     - shell: bash -l -e {0}
       run: |
+        # Fail if on main branch and conda-recipe/meta.yaml exists
+        if [[ "${GITHUB_REF_NAME}" == "main" && -f "conda-recipe/meta.yaml" ]]; then
+          echo "ERROR: conda-recipe/meta.yaml should not be committed to main. Failing build."
+          exit 1
+        fi
+
         set -x
         mkdir -p conda-recipe
+
+        # If meta.yaml exists, use it directly without modifications
+        if [[ -f "conda-recipe/meta.yaml" ]]; then
+          echo "WARN: Using existing conda-recipe/meta.yaml file"
+          set +x
+          exit 0
+        fi
+
         curl -s -L -o conda-recipe/meta.yaml https://raw.githubusercontent.com/conda-forge/genomekit-feedstock/main/recipe/meta.yaml
         export GK_VERSION=$(grep "version = " setup.py | awk -F'"' '{print $2}')
 
         export OS_TYPE=$(uname)
-        # - replace the (non-existent) tarball with local path
-        # - remove the related sha for that tarball
-        # - build for all locally allowed versions of python (conda-recipe/conda_build_config.yaml)
-        # - set the version to the local release-please version (for docs and docker publish)
         if [[ "$OS_TYPE" == "Darwin" ]]; then
-          sed -i '' -E "s|url: https://github.com/deepgenomics/GenomeKit/archive/refs/tags/v.*$|path: ../|1; /sha256: /d; /skip: true /d;s/{% set version = \".+\" %}/{% set version = \"${GK_VERSION}\" %}/" conda-recipe/meta.yaml
+          SED_CMD="sed -i '' -E"
         else
-          sed -i -e    "s|url: https://github.com/deepgenomics/GenomeKit/archive/refs/tags/v.*$|path: ../|1; /sha256: /d; /skip: true /d;s/{% set version = \".\+\" %}/{% set version = \"${GK_VERSION}\" %}/" conda-recipe/meta.yaml
+          SED_CMD="sed -i"
         fi
+        # replace the (non-existent) tarball with local path
+        $SED_CMD "s|url: https://github.com/deepgenomics/GenomeKit/archive/refs/tags/v.*$|path: ../|1" conda-recipe/meta.yaml
+        # remove the related sha for that tarball
+        $SED_CMD "/sha256: /d" conda-recipe/meta.yaml
+        # build for all locally allowed versions of python (conda-recipe/conda_build_config.yaml)
+        $SED_CMD "/skip: true /d" conda-recipe/meta.yaml
+        # set the version to the local release-please version (for docs and docker publish)
+        $SED_CMD "s/{% set version = \".+\" %}/{% set version = \"${GK_VERSION}\" %}/" conda-recipe/meta.yaml
 
         head -10 conda-recipe/meta.yaml
         set +x

From baf56d9f58efd76e58a07253eb757d36215009a5 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Thu, 19 Jun 2025 08:16:22 -0700
Subject: [PATCH 02/52] apply meta.yaml sed modifications on feature branch

---
 .github/actions/curl-meta-yaml/action.yaml | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/.github/actions/curl-meta-yaml/action.yaml b/.github/actions/curl-meta-yaml/action.yaml
index 63a757ee..eac26480 100644
--- a/.github/actions/curl-meta-yaml/action.yaml
+++ b/.github/actions/curl-meta-yaml/action.yaml
@@ -14,14 +14,13 @@ runs:
         set -x
         mkdir -p conda-recipe
 
-        # If meta.yaml exists, use it directly without modifications
+        # If meta.yaml exists, use it (to allow quick iteration in feature branches)
         if [[ -f "conda-recipe/meta.yaml" ]]; then
-          echo "WARN: Using existing conda-recipe/meta.yaml file"
-          set +x
-          exit 0
+          echo "WARN: Using existing conda-recipe/meta.yaml"
+        else
+          curl -s -L -o conda-recipe/meta.yaml https://raw.githubusercontent.com/conda-forge/genomekit-feedstock/main/recipe/meta.yaml
         fi
 
-        curl -s -L -o conda-recipe/meta.yaml https://raw.githubusercontent.com/conda-forge/genomekit-feedstock/main/recipe/meta.yaml
         export GK_VERSION=$(grep "version = " setup.py | awk -F'"' '{print $2}')
 
         export OS_TYPE=$(uname)

From 4bc9af5c78b909890b5e30960c67c3042f31a465 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Wed, 18 Jun 2025 10:43:22 -0700
Subject: [PATCH 03/52] feat: support python 313 (wip)

- fix pyproject.toml to avoid errors
---
 .github/workflows/build-wheels.yaml | 14 ++++++++------
 .github/workflows/run-tests.yaml    |  2 ++
 _pyproject.toml                     |  5 -----
 docs-src/develop.rst                |  6 +++---
 genomekit_dev.yml                   |  6 +++---
 pyproject.toml                      |  7 +++++++
 setup.py                            |  1 +
 7 files changed, 24 insertions(+), 17 deletions(-)
 delete mode 100644 _pyproject.toml
 create mode 100644 pyproject.toml

diff --git a/.github/workflows/build-wheels.yaml b/.github/workflows/build-wheels.yaml
index e849a468..9b553a36 100644
--- a/.github/workflows/build-wheels.yaml
+++ b/.github/workflows/build-wheels.yaml
@@ -46,7 +46,7 @@ jobs:
         name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: '3.13'
 
       - if: ${{ steps.restore_linux_wheels.outputs.cache-hit != 'true' }}
         name: Install cibuildwheel
@@ -57,7 +57,7 @@ jobs:
         run: python -m cibuildwheel --output-dir wheelhouse && ls -l wheelhouse/
         env:
           GK_BUILD_WHEELS: "1"
-          CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-*"
+          CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-* cp313-*"
           CIBW_ARCHS_LINUX: ${{ matrix.arch }}
           CIBW_MANYLINUX_X86_64_IMAGE: manylinux_2_28
           CIBW_MANYLINUX_AARCH64_IMAGE: manylinux_2_28
@@ -65,11 +65,11 @@ jobs:
           CIBW_SKIP: "*-musllinux_*"
 
       - if: ${{ steps.restore_linux_wheels.outputs.cache-hit != 'true' }}
-        name: Test wheels across Python 3.9–3.12
+        name: Test wheels across Python 3.9–3.13
         run: |
           set -euxo pipefail
 
-          for PYVER in 3.9 3.10 3.11 3.12; do
+          for PYVER in 3.9 3.10 3.11 3.12 3.13; do
             PYVER_SHORT=${PYVER/./}
             echo "Testing on Python $PYVER"
 
@@ -119,7 +119,7 @@ jobs:
         name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: '3.13'
 
       - if: ${{ steps.restore_macos_wheels.outputs.cache-hit != 'true' }}
         name: Install cibuildwheel
@@ -131,7 +131,7 @@ jobs:
         env:
           GK_BUILD_WHEELS: "1"
           CIBW_ARCHS_MACOS: x86_64 arm64
-          CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-*"
+          CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-* cp313-*"
 
       - if: ${{ steps.restore_macos_wheels.outputs.cache-hit != 'true' }}
         name: cache macos wheels
@@ -154,10 +154,12 @@ jobs:
           - {"os": "macos-14", "arch": "arm64", "pyver": "3.10", "pyvershort": "310"}
           - {"os": "macos-14", "arch": "arm64", "pyver": "3.11", "pyvershort": "311"}
           - {"os": "macos-14", "arch": "arm64", "pyver": "3.12", "pyvershort": "312"}
+          - {"os": "macos-14", "arch": "arm64", "pyver": "3.13", "pyvershort": "313"}
           - {"os": "macos-13", "arch": "x86_64", "pyver": "3.9", "pyvershort": "39"}
           - {"os": "macos-13", "arch": "x86_64", "pyver": "3.10", "pyvershort": "310"}
           - {"os": "macos-13", "arch": "x86_64", "pyver": "3.11", "pyvershort": "311"}
           - {"os": "macos-13", "arch": "x86_64", "pyver": "3.12", "pyvershort": "312"}
+          - {"os": "macos-13", "arch": "x86_64", "pyver": "3.13", "pyvershort": "313"}
 
     steps:
       - name: Set up Python
diff --git a/.github/workflows/run-tests.yaml b/.github/workflows/run-tests.yaml
index e8319d9a..4a259130 100644
--- a/.github/workflows/run-tests.yaml
+++ b/.github/workflows/run-tests.yaml
@@ -39,6 +39,8 @@ jobs:
           - {"pyver-short": "311", "python-version": "3.11", "platform": "osx-64", "runs-on": "macos-latest"}
           - {"pyver-short": "312", "python-version": "3.12", "platform": "linux-64", "runs-on": "ubuntu-latest"}
           - {"pyver-short": "312", "python-version": "3.12", "platform": "osx-64", "runs-on": "macos-latest"}
+          - {"pyver-short": "313", "python-version": "3.13", "platform": "linux-64", "runs-on": "ubuntu-latest"}
+          - {"pyver-short": "313", "python-version": "3.13", "platform": "osx-64", "runs-on": "macos-latest"}
     runs-on: ${{ matrix.runs-on }}
     steps:
       - uses: actions/checkout@v4
diff --git a/_pyproject.toml b/_pyproject.toml
deleted file mode 100644
index 5a1436f4..00000000
--- a/_pyproject.toml
+++ /dev/null
@@ -1,5 +0,0 @@
-# Specify build system requirements for pip wheel builds.
-# This way is incompatible with conda, which is why the file can't have the name pyproject.toml.
-# The file is renamed to pyproject.toml in Github Actions before starting the pip wheel build.
-[build-system]
-requires = ["setuptools>=42", "wheel", "numpy==2"]
diff --git a/docs-src/develop.rst b/docs-src/develop.rst
index 7581ce00..3ac8f55b 100644
--- a/docs-src/develop.rst
+++ b/docs-src/develop.rst
@@ -29,7 +29,7 @@ On M1 macs, you might need to set up the environment differently::
 
 Build the package in development mode::
 
-    pip install -e .
+    PYTHONPATH=. pip install -e . --no-build-isolation
 
 This builds the C++ extension and copies it into
 your source tree (``genome_kit/_cxx.so``).
@@ -65,7 +65,7 @@ Making changes
 
 If the C/C++ code changed, you must re-run the ``develop`` command::
 
-    pip install -e .
+    PYTHONPATH=. pip install -e . --no-build-isolation
 
 This includes switching branches, merging changes, or editing the C/C++ code
 yourself. *Forgetting this step may lead to unpredictable behaviour.*
@@ -161,7 +161,7 @@ Test data files reside in the source tree under ``tests/data``.
 To build them, you must have registered your source tree in
 develop mode::
 
-    pip install -e .
+    PYTHONPATH=. pip install -e . --no-build-isolation
 
 Now that your source tree is the default `genome_kit` import,
 the ``build`` subcommand will be able to find
diff --git a/genomekit_dev.yml b/genomekit_dev.yml
index 5ba2f85a..d8b6f33c 100644
--- a/genomekit_dev.yml
+++ b/genomekit_dev.yml
@@ -4,8 +4,8 @@ channels:
   - bioconda
 dependencies:
   - appdirs>=1.4.0
-  - numpy <2.0dev0
-  - python>=3.9.0,<3.13.0
+  - numpy
+  - python=3.9.0,<3.14.0
   - tqdm
   - typing-extensions
   - zlib
@@ -16,7 +16,7 @@ dependencies:
   # dev + test dependencies
   - ccache
   - ipython
-  - pyperformance==1.0.4
+  # usage of pyperf was removed internally before open sourcing
   - pytest
   - sphinx
   - sphinx_rtd_theme
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 00000000..6069e17c
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,7 @@
+[build-system]
+requires = [
+    "setuptools>=61",
+    "wheel",
+    "numpy==2"
+]
+build-backend = "setuptools.build_meta"
\ No newline at end of file
diff --git a/setup.py b/setup.py
index 4f245fa5..8abb9dd9 100644
--- a/setup.py
+++ b/setup.py
@@ -53,6 +53,7 @@ def run(self):
             "Programming Language :: Python :: 3.10",
             "Programming Language :: Python :: 3.11",
             "Programming Language :: Python :: 3.12",
+            "Programming Language :: Python :: 3.13",
         ],
         description="GenomeKit is a Python library for fast and easy access to genomic resources such as sequence, data tracks, and annotations.",
         long_description=(Path(__file__).parent / "README.md").read_text(),

From 88ecac158bf665707e6dfbb14daa99db5ff771d2 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Wed, 18 Jun 2025 12:22:16 -0700
Subject: [PATCH 04/52] wip2

---
 .github/actions/curl-meta-yaml/action.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/actions/curl-meta-yaml/action.yaml b/.github/actions/curl-meta-yaml/action.yaml
index eac26480..fe577312 100644
--- a/.github/actions/curl-meta-yaml/action.yaml
+++ b/.github/actions/curl-meta-yaml/action.yaml
@@ -37,6 +37,8 @@ runs:
         $SED_CMD "/skip: true /d" conda-recipe/meta.yaml
         # set the version to the local release-please version (for docs and docker publish)
         $SED_CMD "s/{% set version = \".+\" %}/{% set version = \"${GK_VERSION}\" %}/" conda-recipe/meta.yaml
+        # avoid error "No module named 'setup'" due to "from setup import c_ext" in setup.py
+        $SED_CMD "s/script: {{ PYTHON }} -m pip install --no-deps --ignore-installed ./script: PYTHONPATH=. {{ PYTHON }} -m pip install --no-deps --ignore-installed ./" conda-recipe/meta.yaml
 
         head -10 conda-recipe/meta.yaml
         set +x

From de97eaab9f0ebfffbc41efd023de3ed2d6cefa13 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Wed, 18 Jun 2025 12:53:57 -0700
Subject: [PATCH 05/52] wip3

---
 conda-recipe/conda_build_config.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conda-recipe/conda_build_config.yaml b/conda-recipe/conda_build_config.yaml
index 86572dcb..f35afa4d 100644
--- a/conda-recipe/conda_build_config.yaml
+++ b/conda-recipe/conda_build_config.yaml
@@ -11,3 +11,4 @@ python:
 - '3.10'
 - '3.11'
 - '3.12'
+- '3.13'

From 24f75ac0b7059d0ece9c177f047930bf799cc296 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Wed, 18 Jun 2025 13:18:19 -0700
Subject: [PATCH 06/52] wip4

---
 pyproject.toml => _pyproject.toml | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename pyproject.toml => _pyproject.toml (100%)

diff --git a/pyproject.toml b/_pyproject.toml
similarity index 100%
rename from pyproject.toml
rename to _pyproject.toml

From be315e13557671c1d4769bd2594042a0bac1aa53 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Wed, 18 Jun 2025 13:40:26 -0700
Subject: [PATCH 07/52] wip5

---
 .github/workflows/run-tests.yaml     | 18 +++++++++---------
 conda-recipe/conda_build_config.yaml |  8 ++++----
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/run-tests.yaml b/.github/workflows/run-tests.yaml
index 4a259130..a2876136 100644
--- a/.github/workflows/run-tests.yaml
+++ b/.github/workflows/run-tests.yaml
@@ -31,16 +31,16 @@ jobs:
     strategy:
       matrix:
         include:
-          - {"pyver-short": "39", "python-version": "3.9", "platform": "linux-64", "runs-on": "ubuntu-latest"}
-          - {"pyver-short": "39", "python-version": "3.9", "platform": "osx-64", "runs-on": "macos-latest"}
-          - {"pyver-short": "310", "python-version": "3.10", "platform": "linux-64", "runs-on": "ubuntu-latest"}
-          - {"pyver-short": "310", "python-version": "3.10", "platform": "osx-64", "runs-on": "macos-latest"}
-          - {"pyver-short": "311", "python-version": "3.11", "platform": "linux-64", "runs-on": "ubuntu-latest"}
-          - {"pyver-short": "311", "python-version": "3.11", "platform": "osx-64", "runs-on": "macos-latest"}
-          - {"pyver-short": "312", "python-version": "3.12", "platform": "linux-64", "runs-on": "ubuntu-latest"}
-          - {"pyver-short": "312", "python-version": "3.12", "platform": "osx-64", "runs-on": "macos-latest"}
+#          - {"pyver-short": "39", "python-version": "3.9", "platform": "linux-64", "runs-on": "ubuntu-latest"}
+#          - {"pyver-short": "39", "python-version": "3.9", "platform": "osx-64", "runs-on": "macos-latest"}
+#          - {"pyver-short": "310", "python-version": "3.10", "platform": "linux-64", "runs-on": "ubuntu-latest"}
+#          - {"pyver-short": "310", "python-version": "3.10", "platform": "osx-64", "runs-on": "macos-latest"}
+#          - {"pyver-short": "311", "python-version": "3.11", "platform": "linux-64", "runs-on": "ubuntu-latest"}
+#          - {"pyver-short": "311", "python-version": "3.11", "platform": "osx-64", "runs-on": "macos-latest"}
+#          - {"pyver-short": "312", "python-version": "3.12", "platform": "linux-64", "runs-on": "ubuntu-latest"}
+#          - {"pyver-short": "312", "python-version": "3.12", "platform": "osx-64", "runs-on": "macos-latest"}
           - {"pyver-short": "313", "python-version": "3.13", "platform": "linux-64", "runs-on": "ubuntu-latest"}
-          - {"pyver-short": "313", "python-version": "3.13", "platform": "osx-64", "runs-on": "macos-latest"}
+#          - {"pyver-short": "313", "python-version": "3.13", "platform": "osx-64", "runs-on": "macos-latest"}
     runs-on: ${{ matrix.runs-on }}
     steps:
       - uses: actions/checkout@v4
diff --git a/conda-recipe/conda_build_config.yaml b/conda-recipe/conda_build_config.yaml
index f35afa4d..d3682e4c 100644
--- a/conda-recipe/conda_build_config.yaml
+++ b/conda-recipe/conda_build_config.yaml
@@ -7,8 +7,8 @@ c_stdlib_version:
 - '2.17' # [linux]
 - '14.5' # [osx]
 python:
-- '3.9'
-- '3.10'
-- '3.11'
-- '3.12'
+#- '3.9'
+#- '3.10'
+#- '3.11'
+#- '3.12'
 - '3.13'

From 815af8aa39e26cd9484e1d779d4226bdb42f8910 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Wed, 18 Jun 2025 13:40:32 -0700
Subject: [PATCH 08/52] wip6

---
 conda-recipe/conda_build_config.yaml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/conda-recipe/conda_build_config.yaml b/conda-recipe/conda_build_config.yaml
index d3682e4c..fb4a4c0a 100644
--- a/conda-recipe/conda_build_config.yaml
+++ b/conda-recipe/conda_build_config.yaml
@@ -12,3 +12,8 @@ python:
 #- '3.11'
 #- '3.12'
 - '3.13'
+
+# if not specified, default numpy version is 1.26
+# but py313 not supported for that version of numpy
+numpy:
+  - 2 # [py>=313]
\ No newline at end of file

From 69304ea36c36a017416fa740d991106bc3f9919e Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Thu, 19 Jun 2025 07:23:12 -0700
Subject: [PATCH 09/52] wip7

---
 genomekit_dev.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/genomekit_dev.yml b/genomekit_dev.yml
index d8b6f33c..41708cb7 100644
--- a/genomekit_dev.yml
+++ b/genomekit_dev.yml
@@ -5,7 +5,7 @@ channels:
 dependencies:
   - appdirs>=1.4.0
   - numpy
-  - python=3.9.0,<3.14.0
+  - python>=3.9.0,<3.14.0
   - tqdm
   - typing-extensions
   - zlib

From 0c80c02b52704e36cc2c338cdfb1c48b88ed6104 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Thu, 19 Jun 2025 09:46:40 -0700
Subject: [PATCH 10/52] wip8

---
 conda-recipe/meta.yaml | 68 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 68 insertions(+)
 create mode 100644 conda-recipe/meta.yaml

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
new file mode 100644
index 00000000..42f5b70c
--- /dev/null
+++ b/conda-recipe/meta.yaml
@@ -0,0 +1,68 @@
+{% set version = "7.1.0" %}
+
+package:
+  name: genomekit
+  version: {{ version }}
+
+source:
+  url: https://github.com/deepgenomics/GenomeKit/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: a124ef26234b42da3db8f83d676949b54995b0d2965e4eed22ede3ad8c73506a
+
+build:
+  number: 0
+  script: {{ PYTHON }} -m pip install --no-deps --ignore-installed .
+  skip: true  # [py>312 or py<39]
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - {{ stdlib("c") }}
+    - python                                 # [build_platform != target_platform]
+    - cross-python_{{ target_platform }}     # [build_platform != target_platform]
+    # if not specified, default numpy version is 1.26
+    # but py313 not supported for that version of numpy
+    - numpy ==2                              # [py>=313 and build_platform != target_platform]
+    - numpy                                  # [py<313 and build_platform != target_platform]
+    - setuptools                             # [build_platform != target_platform]
+
+  host:
+    - appdirs
+    - numpy
+    - typing-extensions
+    - zlib
+    - python {{ python }}
+    - pip
+    - setuptools
+
+  run:
+    - appdirs
+    - google-cloud-storage
+    - boto3
+    - typing-extensions
+    - importlib-metadata
+    - tqdm
+    - python {{ python }}
+
+test:
+  imports:
+    - genome_kit
+  requires:
+    - pytest-cov
+    - pip
+  source_files:
+    - tests
+  commands:
+    - pip check
+    - python -m unittest discover
+
+about:
+  doc_url: https://deepgenomics.github.io/GenomeKit/
+  home: https://github.com/deepgenomics/GenomeKit
+  license: "Apache-2.0"
+  license_file: "LICENSE"
+  summary: GenomeKit is a Python library for fast and easy access to genomic resources such as sequence, data tracks, and annotations.
+
+extra:
+  recipe-maintainers:
+    - s22chan
+    - ovesh

From df832cdab54ed89507a2f959b689239db723f05f Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Thu, 19 Jun 2025 09:54:27 -0700
Subject: [PATCH 11/52] wip9

---
 .github/actions/curl-meta-yaml/action.yaml | 2 +-
 conda-recipe/meta.yaml                     | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/actions/curl-meta-yaml/action.yaml b/.github/actions/curl-meta-yaml/action.yaml
index fe577312..f0666a5e 100644
--- a/.github/actions/curl-meta-yaml/action.yaml
+++ b/.github/actions/curl-meta-yaml/action.yaml
@@ -40,5 +40,5 @@ runs:
         # avoid error "No module named 'setup'" due to "from setup import c_ext" in setup.py
         $SED_CMD "s/script: {{ PYTHON }} -m pip install --no-deps --ignore-installed ./script: PYTHONPATH=. {{ PYTHON }} -m pip install --no-deps --ignore-installed ./" conda-recipe/meta.yaml
 
-        head -10 conda-recipe/meta.yaml
+        head -40 conda-recipe/meta.yaml
         set +x
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 42f5b70c..289fbaa0 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -27,7 +27,8 @@ requirements:
 
   host:
     - appdirs
-    - numpy
+    - numpy ==2                              # [py>=313]
+    - numpy                                  # [py<313]
     - typing-extensions
     - zlib
     - python {{ python }}

From 39ed5ad8c15bc64a4972d6621469672e7f1d2d13 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Thu, 19 Jun 2025 10:38:42 -0700
Subject: [PATCH 12/52] wip10

---
 conda-recipe/meta.yaml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 289fbaa0..67889804 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -21,14 +21,12 @@ requirements:
     - cross-python_{{ target_platform }}     # [build_platform != target_platform]
     # if not specified, default numpy version is 1.26
     # but py313 not supported for that version of numpy
-    - numpy ==2                              # [py>=313 and build_platform != target_platform]
-    - numpy                                  # [py<313 and build_platform != target_platform]
+    - numpy ==2
     - setuptools                             # [build_platform != target_platform]
 
   host:
     - appdirs
-    - numpy ==2                              # [py>=313]
-    - numpy                                  # [py<313]
+    - numpy ==2
     - typing-extensions
     - zlib
     - python {{ python }}

From 41127ced93f77138e568ebaf67129a5176399cfe Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Mon, 23 Jun 2025 15:58:01 -0700
Subject: [PATCH 13/52] wip11

---
 conda-recipe/meta.yaml     |  11 ++-
 genome_kit/data_manager.py | 178 +++++++++++++++++++------------------
 genome_kit/vcf_table.py    |   6 +-
 3 files changed, 102 insertions(+), 93 deletions(-)

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 67889804..20ffaac5 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -11,7 +11,7 @@ source:
 build:
   number: 0
   script: {{ PYTHON }} -m pip install --no-deps --ignore-installed .
-  skip: true  # [py>312 or py<39]
+  skip: true  # [py>313 or py<39]
 
 requirements:
   build:
@@ -21,12 +21,14 @@ requirements:
     - cross-python_{{ target_platform }}     # [build_platform != target_platform]
     # if not specified, default numpy version is 1.26
     # but py313 not supported for that version of numpy
-    - numpy ==2
+    - numpy ==2                              # [py>=313 and build_platform != target_platform]
+    - numpy                                  # [py<313 and build_platform != target_platform]
     - setuptools                             # [build_platform != target_platform]
 
   host:
     - appdirs
-    - numpy ==2
+    - numpy ==2 # [py>=313]
+    - numpy     # [py<313]
     - typing-extensions
     - zlib
     - python {{ python }}
@@ -35,7 +37,8 @@ requirements:
 
   run:
     - appdirs
-    - google-cloud-storage
+    # google-cloud-storage breaks the build on py313
+    - google-cloud-storage # [py<313]
     - boto3
     - typing-extensions
     - importlib-metadata
diff --git a/genome_kit/data_manager.py b/genome_kit/data_manager.py
index 679ac30d..5f94bc22 100644
--- a/genome_kit/data_manager.py
+++ b/genome_kit/data_manager.py
@@ -11,7 +11,12 @@
 from pathlib import Path
 from typing import Dict, Any
 
-from google.cloud import storage
+_SUPPORT_GCS = True
+try:
+    from google.cloud import storage
+except ImportError:
+    # google.cloud breaks build on py313
+    _SUPPORT_GCS = False
 import boto3
 from botocore import UNSIGNED
 from botocore.config import Config
@@ -167,109 +172,110 @@ def FileIO(filename, desc, mode, size, quiet):
             )
             yield decorated
 
-class GCSDataManager(DataManager):
-    """A minimal data manager implementation that retrieves files from a GCS bucket."""
-    def __init__(self, data_dir: str, bucket_name: str):
-        """
-        Args:
-            data_dir: location where local files are cached
-            bucket_name: GCS bucket
-        """
-        self._bucket_name = bucket_name
-        super().__init__(data_dir)
+if _SUPPORT_GCS is True:
+    class GCSDataManager(DataManager):
+        """A minimal data manager implementation that retrieves files from a GCS bucket."""
+        def __init__(self, data_dir: str, bucket_name: str):
+            """
+            Args:
+                data_dir: location where local files are cached
+                bucket_name: GCS bucket
+            """
+            self._bucket_name = bucket_name
+            super().__init__(data_dir)
+
+        @property
+        def bucket(self):
+            if not hasattr(self, "_bucket"):
+                gcloud_client = storage.Client()
+                try:
+                    self._bucket = gcloud_client.bucket(self._bucket_name, user_project=os.environ.get("GENOMEKIT_GCS_BILLING_PROJECT", None))
+                except Exception as e:
+                    # give the user a hint in case of permission errors
+                    print(e, file=sys.stderr)
+                    raise
+
+            return self._bucket
+
+        def get_file(self, filename: str) -> str:
+            local_path = Path(self.data_dir, filename)
+
+            if local_path.exists():
+                return str(local_path)
 
-    @property
-    def bucket(self):
-        if not hasattr(self, "_bucket"):
-            gcloud_client = storage.Client()
             try:
-                self._bucket = gcloud_client.bucket(self._bucket_name, user_project=os.environ.get("GENOMEKIT_GCS_BILLING_PROJECT", None))
+                blob = self.bucket.blob(filename)
+                if not blob.exists():
+                    raise FileNotFoundError(f"File '{filename}' not found in the GCS bucket")
             except Exception as e:
-                # give the user a hint in case of permission errors
-                print(e, file=sys.stderr)
+                if "GENOMEKIT_TRACE" in os.environ:
+                    # give the user a hint in case of permission errors
+                    print(e, file=sys.stderr)
                 raise
 
-        return self._bucket
-
-    def get_file(self, filename: str) -> str:
-        local_path = Path(self.data_dir, filename)
+            # form a temporary filename to make the download safe
+            temp_file = tempfile.NamedTemporaryFile(delete=False, mode="wb", dir=self.data_dir, prefix=filename, suffix=".part")
+            temp_file_path = str(Path(self.data_dir, temp_file.name))
+            try:
+                temp_file.close()
+                with FileIO(temp_file_path, filename, "wb", blob.size, quiet=False) as f:
+                    blob.download_to_file(f)
+            except:
+                os.remove(temp_file_path)
+                raise
+            # atomically (on POSIX) rename the file to the real one
+            os.rename(temp_file_path, local_path)
 
-        if local_path.exists():
             return str(local_path)
 
-        try:
-            blob = self.bucket.blob(filename)
-            if not blob.exists():
-                raise FileNotFoundError(f"File '{filename}' not found in the GCS bucket")
-        except Exception as e:
-            if "GENOMEKIT_TRACE" in os.environ:
-                # give the user a hint in case of permission errors
-                print(e, file=sys.stderr)
-            raise
+        def _remote_equal(self, blob: storage.Blob, file_path: Path) -> bool:
+            remote_checksum = base64.b64decode(blob.md5_hash).hex()
+            with open(file_path, 'rb') as f:
+                local_checksum = _hashfile(f, hashlib.md5())
+            return remote_checksum == local_checksum
 
-        # form a temporary filename to make the download safe
-        temp_file = tempfile.NamedTemporaryFile(delete=False, mode="wb", dir=self.data_dir, prefix=filename, suffix=".part")
-        temp_file_path = str(Path(self.data_dir, temp_file.name))
-        try:
-            temp_file.close()
-            with FileIO(temp_file_path, filename, "wb", blob.size, quiet=False) as f:
-                blob.download_to_file(f)
-        except:
-            os.remove(temp_file_path)
-            raise
-        # atomically (on POSIX) rename the file to the real one
-        os.rename(temp_file_path, local_path)
-
-        return str(local_path)
-
-    def _remote_equal(self, blob: storage.Blob, file_path: Path) -> bool:
-        remote_checksum = base64.b64decode(blob.md5_hash).hex()
-        with open(file_path, 'rb') as f:
-            local_checksum = _hashfile(f, hashlib.md5())
-        return remote_checksum == local_checksum
-
-    def upload_file(self, filepath: str, filename: str, metadata: Dict[str, str]=None):
-        blob = self.bucket.blob(filename)
-
-        if blob.exists():
-            blob.reload()
-            if self._remote_equal(blob, Path(filepath)):
-                logger.info(f"File '{filename}' already exists in the GCS bucket and is identical, skipping.")
-                return
+        def upload_file(self, filepath: str, filename: str, metadata: Dict[str, str]=None):
+            blob = self.bucket.blob(filename)
 
-            if "GK_UPLOAD_ALLOW_OVERWRITE" not in os.environ:
-                raise ValueError(f"File '{filename}' already exists in the GCS bucket."
-                                 "Set GK_UPLOAD_ALLOW_OVERWRITE=1 to overwrite.")
+            if blob.exists():
+                blob.reload()
+                if self._remote_equal(blob, Path(filepath)):
+                    logger.info(f"File '{filename}' already exists in the GCS bucket and is identical, skipping.")
+                    return
+
+                if "GK_UPLOAD_ALLOW_OVERWRITE" not in os.environ:
+                    raise ValueError(f"File '{filename}' already exists in the GCS bucket."
+                                     "Set GK_UPLOAD_ALLOW_OVERWRITE=1 to overwrite.")
+                else:
+                    logger.warning(f"Overwriting '{filename}' on the server.")
+
+                if blob.metadata is None:
+                    blob.metadata = metadata
+                else:
+                    blob.metadata.update(metadata or {})
             else:
-                logger.warning(f"Overwriting '{filename}' on the server.")
-
-            if blob.metadata is None:
                 blob.metadata = metadata
-            else:
-                blob.metadata.update(metadata or {})
-        else:
-            blob.metadata = metadata
 
-        with FileIO(filepath, filename, "rb", os.path.getsize(filepath), quiet=False) as f:
-            blob.upload_from_file(f)
+            with FileIO(filepath, filename, "rb", os.path.getsize(filepath), quiet=False) as f:
+                blob.upload_from_file(f)
 
-    @lru_cache
-    def list_available_genomes(self):
-        names = set()
+        @lru_cache
+        def list_available_genomes(self):
+            names = set()
 
-        def get_genomes(filenames):
-            return (
-                name.rpartition(".")[0]
-                for name in filenames
-                if name.endswith(".2bit") or name.endswith(".cfg")
-            )
+            def get_genomes(filenames):
+                return (
+                    name.rpartition(".")[0]
+                    for name in filenames
+                    if name.endswith(".2bit") or name.endswith(".cfg")
+                )
 
-        names.update(get_genomes(os.listdir(self.data_dir)))
+            names.update(get_genomes(os.listdir(self.data_dir)))
 
-        blobs = self.bucket.list_blobs()
-        names.update(get_genomes(blob.name for blob in blobs))
+            blobs = self.bucket.list_blobs()
+            names.update(get_genomes(blob.name for blob in blobs))
 
-        return sorted(names)
+            return sorted(names)
 
 class DefaultDataManager(DataManager):
     """A minimal data manager implementation that retrieves files from a S3 bucket.
diff --git a/genome_kit/vcf_table.py b/genome_kit/vcf_table.py
index b8afb4bd..ac590361 100644
--- a/genome_kit/vcf_table.py
+++ b/genome_kit/vcf_table.py
@@ -5,7 +5,7 @@
 import os
 import subprocess
 import tempfile
-from distutils.spawn import find_executable
+import shutil
 from typing import Optional, Union
 from typing_extensions import Literal
 
@@ -26,7 +26,7 @@ def _dump_fasta(genome, chrom_mapper):
     """Dumps a FASTA containing the DNA sequence of refg, indexes it, and returns a context
     that can be treated as the path to the fasta. The temporaries are deleted once the
     context is closed."""
-    samtools = find_executable("samtools")
+    samtools = shutil.which("samtools")
     if not samtools:
         raise RuntimeError("samtools must be installed in order to normalize VCFs")  # pragma: no cover
 
@@ -216,7 +216,7 @@ def open_clinvar(vcfpath):
         else:
             if normalize:
                 # Check requirements
-                bcftools = find_executable("bcftools")
+                bcftools = shutil.which("bcftools")
                 if not bcftools:
                     raise RuntimeError("bcftools must be installed to normalize VCFs")  # pragma: no cover
 

From fd40b03ca45ceef7bce84b0ff9ae768acd86574e Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Mon, 23 Jun 2025 16:19:26 -0700
Subject: [PATCH 14/52] wip12

---
 genome_kit/data_manager.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/genome_kit/data_manager.py b/genome_kit/data_manager.py
index 5f94bc22..bacde505 100644
--- a/genome_kit/data_manager.py
+++ b/genome_kit/data_manager.py
@@ -172,7 +172,10 @@ def FileIO(filename, desc, mode, size, quiet):
             )
             yield decorated
 
-if _SUPPORT_GCS is True:
+if _SUPPORT_GCS is False:
+    class GCSDataManager(DataManager):
+        pass
+else:
     class GCSDataManager(DataManager):
         """A minimal data manager implementation that retrieves files from a GCS bucket."""
         def __init__(self, data_dir: str, bucket_name: str):

From 6b601e121c4a2c2f9cabee7810a0727f6b47c912 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Mon, 23 Jun 2025 22:13:43 -0700
Subject: [PATCH 15/52] wip13

---
 .github/workflows/run-tests.yaml | 2 +-
 conda-recipe/meta.yaml           | 8 ++------
 genome_kit/data_manager.py       | 3 ++-
 3 files changed, 5 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/run-tests.yaml b/.github/workflows/run-tests.yaml
index a2876136..f9f31785 100644
--- a/.github/workflows/run-tests.yaml
+++ b/.github/workflows/run-tests.yaml
@@ -40,7 +40,7 @@ jobs:
 #          - {"pyver-short": "312", "python-version": "3.12", "platform": "linux-64", "runs-on": "ubuntu-latest"}
 #          - {"pyver-short": "312", "python-version": "3.12", "platform": "osx-64", "runs-on": "macos-latest"}
           - {"pyver-short": "313", "python-version": "3.13", "platform": "linux-64", "runs-on": "ubuntu-latest"}
-#          - {"pyver-short": "313", "python-version": "3.13", "platform": "osx-64", "runs-on": "macos-latest"}
+          - {"pyver-short": "313", "python-version": "3.13", "platform": "osx-64", "runs-on": "macos-latest"}
     runs-on: ${{ matrix.runs-on }}
     steps:
       - uses: actions/checkout@v4
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 20ffaac5..c08e1169 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -19,16 +19,12 @@ requirements:
     - {{ stdlib("c") }}
     - python                                 # [build_platform != target_platform]
     - cross-python_{{ target_platform }}     # [build_platform != target_platform]
-    # if not specified, default numpy version is 1.26
-    # but py313 not supported for that version of numpy
-    - numpy ==2                              # [py>=313 and build_platform != target_platform]
-    - numpy                                  # [py<313 and build_platform != target_platform]
+    - numpy                                  # [build_platform != target_platform]
     - setuptools                             # [build_platform != target_platform]
 
   host:
     - appdirs
-    - numpy ==2 # [py>=313]
-    - numpy     # [py<313]
+    - numpy
     - typing-extensions
     - zlib
     - python {{ python }}
diff --git a/genome_kit/data_manager.py b/genome_kit/data_manager.py
index bacde505..96b62279 100644
--- a/genome_kit/data_manager.py
+++ b/genome_kit/data_manager.py
@@ -174,7 +174,8 @@ def FileIO(filename, desc, mode, size, quiet):
 
 if _SUPPORT_GCS is False:
     class GCSDataManager(DataManager):
-        pass
+        def __init__(self, data_dir: str, bucket_name: str):
+            raise NotImplementedError("GCS support not available on py313")
 else:
     class GCSDataManager(DataManager):
         """A minimal data manager implementation that retrieves files from a GCS bucket."""

From 201809638e92e9558a491a734a034efdf011bbc1 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Mon, 23 Jun 2025 22:18:02 -0700
Subject: [PATCH 16/52] wip14

---
 conda-recipe/meta.yaml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index c08e1169..40d58e75 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -19,7 +19,10 @@ requirements:
     - {{ stdlib("c") }}
     - python                                 # [build_platform != target_platform]
     - cross-python_{{ target_platform }}     # [build_platform != target_platform]
-    - numpy                                  # [build_platform != target_platform]
+    # if not specified, default numpy version is 1.26
+    # but py313 not supported for that version of numpy
+    - numpy ==2                              # [py>=313 and build_platform != target_platform]
+    - numpy                                  # [py<313 and build_platform != target_platform]
     - setuptools                             # [build_platform != target_platform]
 
   host:

From b6b671107df669e0311deabb6ae46d877faa4989 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Tue, 24 Jun 2025 07:16:38 -0700
Subject: [PATCH 17/52] wip15

---
 conda-recipe/meta.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 40d58e75..e8173c01 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -21,13 +21,13 @@ requirements:
     - cross-python_{{ target_platform }}     # [build_platform != target_platform]
     # if not specified, default numpy version is 1.26
     # but py313 not supported for that version of numpy
-    - numpy ==2                              # [py>=313 and build_platform != target_platform]
-    - numpy                                  # [py<313 and build_platform != target_platform]
+    - numpy                                  # [build_platform != target_platform]
     - setuptools                             # [build_platform != target_platform]
 
   host:
     - appdirs
-    - numpy
+    - numpy ==2 # [py>=313]
+    - numpy     # [py<313]
     - typing-extensions
     - zlib
     - python {{ python }}

From c2235ffd70de10ef64f3809a794dd7672e7b1b4e Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Tue, 24 Jun 2025 07:36:39 -0700
Subject: [PATCH 18/52] wip16

---
 conda-recipe/conda_build_config.yaml | 7 +------
 conda-recipe/meta.yaml               | 3 +--
 2 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/conda-recipe/conda_build_config.yaml b/conda-recipe/conda_build_config.yaml
index fb4a4c0a..3a26865c 100644
--- a/conda-recipe/conda_build_config.yaml
+++ b/conda-recipe/conda_build_config.yaml
@@ -11,9 +11,4 @@ python:
 #- '3.10'
 #- '3.11'
 #- '3.12'
-- '3.13'
-
-# if not specified, default numpy version is 1.26
-# but py313 not supported for that version of numpy
-numpy:
-  - 2 # [py>=313]
\ No newline at end of file
+- '3.13'
\ No newline at end of file
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index e8173c01..e9622012 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -19,13 +19,12 @@ requirements:
     - {{ stdlib("c") }}
     - python                                 # [build_platform != target_platform]
     - cross-python_{{ target_platform }}     # [build_platform != target_platform]
-    # if not specified, default numpy version is 1.26
-    # but py313 not supported for that version of numpy
     - numpy                                  # [build_platform != target_platform]
     - setuptools                             # [build_platform != target_platform]
 
   host:
     - appdirs
+    # I don't know why, but if not specified, conda selects numpy v1.26, incompatible with py313
     - numpy ==2 # [py>=313]
     - numpy     # [py<313]
     - typing-extensions

From b6e7d90731b8c8998cedd9ff6f8b7a717ac31b90 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Tue, 24 Jun 2025 08:50:57 -0700
Subject: [PATCH 19/52] wip17

---
 conda-recipe/conda_build_config.yaml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/conda-recipe/conda_build_config.yaml b/conda-recipe/conda_build_config.yaml
index 3a26865c..3a46935a 100644
--- a/conda-recipe/conda_build_config.yaml
+++ b/conda-recipe/conda_build_config.yaml
@@ -11,4 +11,7 @@ python:
 #- '3.10'
 #- '3.11'
 #- '3.12'
-- '3.13'
\ No newline at end of file
+- '3.13'
+
+numpy:
+  - 2 # [py>=313]
\ No newline at end of file

From c310459f25479de944aad7e31dbd050f4611a3cb Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Tue, 24 Jun 2025 10:19:53 -0700
Subject: [PATCH 20/52] wip18

---
 conda-recipe/meta.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index e9622012..b74544c4 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -24,9 +24,9 @@ requirements:
 
   host:
     - appdirs
-    # I don't know why, but if not specified, conda selects numpy v1.26, incompatible with py313
-    - numpy ==2 # [py>=313]
-    - numpy     # [py<313]
+    # don't know why, but if not specified, conda selects numpy v1.26, incompatible with py313
+    - {{ numpy }} # [py>=313]
+    - numpy # [py<313]
     - typing-extensions
     - zlib
     - python {{ python }}

From acd28641449ebc744bc17e767e96ca2422da14b9 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Tue, 24 Jun 2025 10:55:48 -0700
Subject: [PATCH 21/52] wip19

---
 conda-recipe/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index b74544c4..52db17a6 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -25,7 +25,7 @@ requirements:
   host:
     - appdirs
     # don't know why, but if not specified, conda selects numpy v1.26, incompatible with py313
-    - {{ numpy }} # [py>=313]
+    - numpy {{ numpy }} # [py>=313]
     - numpy # [py<313]
     - typing-extensions
     - zlib

From 17e9104f7e65bdae10674a283d548f77c3642d1b Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Tue, 24 Jun 2025 11:04:03 -0700
Subject: [PATCH 22/52] wip20

---
 conda-recipe/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 52db17a6..b5819cd3 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -25,8 +25,8 @@ requirements:
   host:
     - appdirs
     # don't know why, but if not specified, conda selects numpy v1.26, incompatible with py313
-    - numpy {{ numpy }} # [py>=313]
-    - numpy # [py<313]
+    - numpy ==2 # [py>=313]
+    - numpy     # [py<313]
     - typing-extensions
     - zlib
     - python {{ python }}

From 1ac0a0f050ce66b7627efeefaa9371e375644b65 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Tue, 24 Jun 2025 13:57:34 -0700
Subject: [PATCH 23/52] wip21

---
 .github/workflows/run-tests.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/run-tests.yaml b/.github/workflows/run-tests.yaml
index f9f31785..c2fe542e 100644
--- a/.github/workflows/run-tests.yaml
+++ b/.github/workflows/run-tests.yaml
@@ -79,7 +79,7 @@ jobs:
           set -x
           if [ ! -d "${HOME}/micromamba/envs/test" ]; then
             micromamba create -yqn test -c conda-forge \
-              boa==0.16.0 mamba==1.5.7 conda==24.1.2 coverage
+              boa==0.16.0 mamba==1.5.7 conda==24.1.2
           fi
           set +x
 

From a5dc958a3959f4dff1febd45155712588090b0f6 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Wed, 25 Jun 2025 11:52:03 -0700
Subject: [PATCH 24/52] wip22

---
 .github/workflows/run-tests.yaml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/run-tests.yaml b/.github/workflows/run-tests.yaml
index c2fe542e..d0df08c4 100644
--- a/.github/workflows/run-tests.yaml
+++ b/.github/workflows/run-tests.yaml
@@ -37,8 +37,8 @@ jobs:
 #          - {"pyver-short": "310", "python-version": "3.10", "platform": "osx-64", "runs-on": "macos-latest"}
 #          - {"pyver-short": "311", "python-version": "3.11", "platform": "linux-64", "runs-on": "ubuntu-latest"}
 #          - {"pyver-short": "311", "python-version": "3.11", "platform": "osx-64", "runs-on": "macos-latest"}
-#          - {"pyver-short": "312", "python-version": "3.12", "platform": "linux-64", "runs-on": "ubuntu-latest"}
-#          - {"pyver-short": "312", "python-version": "3.12", "platform": "osx-64", "runs-on": "macos-latest"}
+          - {"pyver-short": "312", "python-version": "3.12", "platform": "linux-64", "runs-on": "ubuntu-latest"}
+          - {"pyver-short": "312", "python-version": "3.12", "platform": "osx-64", "runs-on": "macos-latest"}
           - {"pyver-short": "313", "python-version": "3.13", "platform": "linux-64", "runs-on": "ubuntu-latest"}
           - {"pyver-short": "313", "python-version": "3.13", "platform": "osx-64", "runs-on": "macos-latest"}
     runs-on: ${{ matrix.runs-on }}
@@ -79,6 +79,8 @@ jobs:
           set -x
           if [ ! -d "${HOME}/micromamba/envs/test" ]; then
             micromamba create -yqn test -c conda-forge \
+              # inconsistently got "coverage 7.9.1 is not supported on this platform" so removed
+              # (not needed?)
               boa==0.16.0 mamba==1.5.7 conda==24.1.2
           fi
           set +x

From 5fc7559eb7609923a0d7411480525de5092ef209 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Wed, 25 Jun 2025 12:17:18 -0700
Subject: [PATCH 25/52] wip23

---
 .github/workflows/run-tests.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/run-tests.yaml b/.github/workflows/run-tests.yaml
index d0df08c4..9ad6db92 100644
--- a/.github/workflows/run-tests.yaml
+++ b/.github/workflows/run-tests.yaml
@@ -91,6 +91,7 @@ jobs:
         run: |
           set -x
           micromamba activate test
+          conda --version
           conda index ~/conda-bld
           files=(~/conda-bld/*/*py${{ matrix.pyver-short }}*.tar.bz2)
           if [ ! -e "${files[0]}" ]; then

From 736a0f108193dfaa2f41a0ac794bf76774728de0 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Wed, 25 Jun 2025 13:40:09 -0700
Subject: [PATCH 26/52] wip24

---
 .github/workflows/run-tests.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/run-tests.yaml b/.github/workflows/run-tests.yaml
index 9ad6db92..7c49e0dd 100644
--- a/.github/workflows/run-tests.yaml
+++ b/.github/workflows/run-tests.yaml
@@ -77,10 +77,10 @@ jobs:
         shell: bash -l -e {0}
         run: |
           set -x
+          # inconsistently got "coverage 7.9.1 is not supported on this platform" so removed
+          # (not needed?)
           if [ ! -d "${HOME}/micromamba/envs/test" ]; then
             micromamba create -yqn test -c conda-forge \
-              # inconsistently got "coverage 7.9.1 is not supported on this platform" so removed
-              # (not needed?)
               boa==0.16.0 mamba==1.5.7 conda==24.1.2
           fi
           set +x

From c3cce0aaf871a864643e52e3511a0b0074c85e17 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Wed, 25 Jun 2025 14:08:27 -0700
Subject: [PATCH 27/52] wip25

---
 conda-recipe/conda_build_config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conda-recipe/conda_build_config.yaml b/conda-recipe/conda_build_config.yaml
index 3a46935a..ed09d058 100644
--- a/conda-recipe/conda_build_config.yaml
+++ b/conda-recipe/conda_build_config.yaml
@@ -10,7 +10,7 @@ python:
 #- '3.9'
 #- '3.10'
 #- '3.11'
-#- '3.12'
+- '3.12'
 - '3.13'
 
 numpy:

From f7f1ab56eaa2b49588795c9282cf88c1289411fe Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Wed, 25 Jun 2025 14:28:44 -0700
Subject: [PATCH 28/52] wip26

---
 .github/workflows/run-tests.yaml     | 13 ++++++-------
 conda-recipe/conda_build_config.yaml |  6 +++---
 2 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/run-tests.yaml b/.github/workflows/run-tests.yaml
index 7c49e0dd..c2a916c5 100644
--- a/.github/workflows/run-tests.yaml
+++ b/.github/workflows/run-tests.yaml
@@ -31,12 +31,12 @@ jobs:
     strategy:
       matrix:
         include:
-#          - {"pyver-short": "39", "python-version": "3.9", "platform": "linux-64", "runs-on": "ubuntu-latest"}
-#          - {"pyver-short": "39", "python-version": "3.9", "platform": "osx-64", "runs-on": "macos-latest"}
-#          - {"pyver-short": "310", "python-version": "3.10", "platform": "linux-64", "runs-on": "ubuntu-latest"}
-#          - {"pyver-short": "310", "python-version": "3.10", "platform": "osx-64", "runs-on": "macos-latest"}
-#          - {"pyver-short": "311", "python-version": "3.11", "platform": "linux-64", "runs-on": "ubuntu-latest"}
-#          - {"pyver-short": "311", "python-version": "3.11", "platform": "osx-64", "runs-on": "macos-latest"}
+          - {"pyver-short": "39", "python-version": "3.9", "platform": "linux-64", "runs-on": "ubuntu-latest"}
+          - {"pyver-short": "39", "python-version": "3.9", "platform": "osx-64", "runs-on": "macos-latest"}
+          - {"pyver-short": "310", "python-version": "3.10", "platform": "linux-64", "runs-on": "ubuntu-latest"}
+          - {"pyver-short": "310", "python-version": "3.10", "platform": "osx-64", "runs-on": "macos-latest"}
+          - {"pyver-short": "311", "python-version": "3.11", "platform": "linux-64", "runs-on": "ubuntu-latest"}
+          - {"pyver-short": "311", "python-version": "3.11", "platform": "osx-64", "runs-on": "macos-latest"}
           - {"pyver-short": "312", "python-version": "3.12", "platform": "linux-64", "runs-on": "ubuntu-latest"}
           - {"pyver-short": "312", "python-version": "3.12", "platform": "osx-64", "runs-on": "macos-latest"}
           - {"pyver-short": "313", "python-version": "3.13", "platform": "linux-64", "runs-on": "ubuntu-latest"}
@@ -91,7 +91,6 @@ jobs:
         run: |
           set -x
           micromamba activate test
-          conda --version
           conda index ~/conda-bld
           files=(~/conda-bld/*/*py${{ matrix.pyver-short }}*.tar.bz2)
           if [ ! -e "${files[0]}" ]; then
diff --git a/conda-recipe/conda_build_config.yaml b/conda-recipe/conda_build_config.yaml
index ed09d058..61c3e60a 100644
--- a/conda-recipe/conda_build_config.yaml
+++ b/conda-recipe/conda_build_config.yaml
@@ -7,9 +7,9 @@ c_stdlib_version:
 - '2.17' # [linux]
 - '14.5' # [osx]
 python:
-#- '3.9'
-#- '3.10'
-#- '3.11'
+- '3.9'
+- '3.10'
+- '3.11'
 - '3.12'
 - '3.13'
 

From 601a50d388761dca216b2fde2adf83252f0d310b Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Wed, 25 Jun 2025 14:59:41 -0700
Subject: [PATCH 29/52] wip27

---
 .github/workflows/run-tests.yaml     | 16 ++++++++--------
 conda-recipe/conda_build_config.yaml | 11 ++++-------
 conda-recipe/meta.yaml               |  4 ++--
 3 files changed, 14 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/run-tests.yaml b/.github/workflows/run-tests.yaml
index c2a916c5..4c6b39a0 100644
--- a/.github/workflows/run-tests.yaml
+++ b/.github/workflows/run-tests.yaml
@@ -31,14 +31,14 @@ jobs:
     strategy:
       matrix:
         include:
-          - {"pyver-short": "39", "python-version": "3.9", "platform": "linux-64", "runs-on": "ubuntu-latest"}
-          - {"pyver-short": "39", "python-version": "3.9", "platform": "osx-64", "runs-on": "macos-latest"}
-          - {"pyver-short": "310", "python-version": "3.10", "platform": "linux-64", "runs-on": "ubuntu-latest"}
-          - {"pyver-short": "310", "python-version": "3.10", "platform": "osx-64", "runs-on": "macos-latest"}
-          - {"pyver-short": "311", "python-version": "3.11", "platform": "linux-64", "runs-on": "ubuntu-latest"}
-          - {"pyver-short": "311", "python-version": "3.11", "platform": "osx-64", "runs-on": "macos-latest"}
-          - {"pyver-short": "312", "python-version": "3.12", "platform": "linux-64", "runs-on": "ubuntu-latest"}
-          - {"pyver-short": "312", "python-version": "3.12", "platform": "osx-64", "runs-on": "macos-latest"}
+#          - {"pyver-short": "39", "python-version": "3.9", "platform": "linux-64", "runs-on": "ubuntu-latest"}
+#          - {"pyver-short": "39", "python-version": "3.9", "platform": "osx-64", "runs-on": "macos-latest"}
+#          - {"pyver-short": "310", "python-version": "3.10", "platform": "linux-64", "runs-on": "ubuntu-latest"}
+#          - {"pyver-short": "310", "python-version": "3.10", "platform": "osx-64", "runs-on": "macos-latest"}
+#          - {"pyver-short": "311", "python-version": "3.11", "platform": "linux-64", "runs-on": "ubuntu-latest"}
+#          - {"pyver-short": "311", "python-version": "3.11", "platform": "osx-64", "runs-on": "macos-latest"}
+#          - {"pyver-short": "312", "python-version": "3.12", "platform": "linux-64", "runs-on": "ubuntu-latest"}
+#          - {"pyver-short": "312", "python-version": "3.12", "platform": "osx-64", "runs-on": "macos-latest"}
           - {"pyver-short": "313", "python-version": "3.13", "platform": "linux-64", "runs-on": "ubuntu-latest"}
           - {"pyver-short": "313", "python-version": "3.13", "platform": "osx-64", "runs-on": "macos-latest"}
     runs-on: ${{ matrix.runs-on }}
diff --git a/conda-recipe/conda_build_config.yaml b/conda-recipe/conda_build_config.yaml
index 61c3e60a..d3682e4c 100644
--- a/conda-recipe/conda_build_config.yaml
+++ b/conda-recipe/conda_build_config.yaml
@@ -7,11 +7,8 @@ c_stdlib_version:
 - '2.17' # [linux]
 - '14.5' # [osx]
 python:
-- '3.9'
-- '3.10'
-- '3.11'
-- '3.12'
+#- '3.9'
+#- '3.10'
+#- '3.11'
+#- '3.12'
 - '3.13'
-
-numpy:
-  - 2 # [py>=313]
\ No newline at end of file
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index b5819cd3..ca485591 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -25,8 +25,8 @@ requirements:
   host:
     - appdirs
     # don't know why, but if not specified, conda selects numpy v1.26, incompatible with py313
-    - numpy ==2 # [py>=313]
-    - numpy     # [py<313]
+    - numpy 2 # [py>=313]
+    - numpy   # [py<313]
     - typing-extensions
     - zlib
     - python {{ python }}

From 81a3923f73556420fde520fea934bd7d0c5c4ae6 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Thu, 26 Jun 2025 11:56:43 -0700
Subject: [PATCH 30/52] wip28

---
 .github/workflows/run-tests.yaml | 4 +---
 conda-recipe/meta.yaml           | 1 -
 2 files changed, 1 insertion(+), 4 deletions(-)

diff --git a/.github/workflows/run-tests.yaml b/.github/workflows/run-tests.yaml
index 4c6b39a0..f9f31785 100644
--- a/.github/workflows/run-tests.yaml
+++ b/.github/workflows/run-tests.yaml
@@ -77,11 +77,9 @@ jobs:
         shell: bash -l -e {0}
         run: |
           set -x
-          # inconsistently got "coverage 7.9.1 is not supported on this platform" so removed
-          # (not needed?)
           if [ ! -d "${HOME}/micromamba/envs/test" ]; then
             micromamba create -yqn test -c conda-forge \
-              boa==0.16.0 mamba==1.5.7 conda==24.1.2
+              boa==0.16.0 mamba==1.5.7 conda==24.1.2 coverage
           fi
           set +x
 
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index ca485591..94d77955 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -47,7 +47,6 @@ test:
   imports:
     - genome_kit
   requires:
-    - pytest-cov
     - pip
   source_files:
     - tests

From 002b0ce229c57c6852681da562600f9effc77885 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Thu, 26 Jun 2025 12:42:08 -0700
Subject: [PATCH 31/52] wip29

---
 .github/actions/build-gk/action.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/actions/build-gk/action.yaml b/.github/actions/build-gk/action.yaml
index 731a5f87..d44eca81 100644
--- a/.github/actions/build-gk/action.yaml
+++ b/.github/actions/build-gk/action.yaml
@@ -94,6 +94,6 @@ runs:
       id: save_gk_pkg
       uses: actions/cache/save@v4
       with:
-        key: mamba-env-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('.github/workflows/run-tests.yaml', '.github/actions/**', 'conda-recipe/**', 'src/**', 'genome_kit/**', 'setup.py', 'setup/**', 'tests/**') }}
+        key: gk-tarballs-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('.github/workflows/run-tests.yaml', '.github/actions/**', 'conda-recipe/**', 'src/**', 'genome_kit/**', 'setup.py', 'setup/**', 'tests/**') }}
         path: |
           ~/conda-bld

From c41e6ced62fccadf325e8aad1a4bef6e86b9eeff Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Thu, 26 Jun 2025 13:12:56 -0700
Subject: [PATCH 32/52] wip30

---
 .github/actions/build-gk/action.yaml | 2 +-
 .github/workflows/dockerize.yaml     | 2 +-
 .github/workflows/publish-docs.yaml  | 2 +-
 .github/workflows/run-tests.yaml     | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/actions/build-gk/action.yaml b/.github/actions/build-gk/action.yaml
index d44eca81..19c54101 100644
--- a/.github/actions/build-gk/action.yaml
+++ b/.github/actions/build-gk/action.yaml
@@ -24,7 +24,7 @@ runs:
       id: restore_gk_pkg
       uses: actions/cache/restore@v4
       with:
-        key: mamba-env-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('.github/workflows/run-tests.yaml', '.github/actions/**', 'conda-recipe/**', 'src/**', 'genome_kit/**', 'setup.py', 'setup/**', 'tests/**') }}
+        key: gk-tarballs-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('.github/workflows/run-tests.yaml', '.github/actions/**', 'conda-recipe/**', 'src/**', 'genome_kit/**', 'setup.py', 'setup/**', 'tests/**') }}
         path: |
           ~/conda-bld
 
diff --git a/.github/workflows/dockerize.yaml b/.github/workflows/dockerize.yaml
index 55780aec..0f4aa8f1 100644
--- a/.github/workflows/dockerize.yaml
+++ b/.github/workflows/dockerize.yaml
@@ -39,7 +39,7 @@ jobs:
         id: restore_gk_pkg
         uses: actions/cache/restore@v4
         with:
-          key: mamba-env-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('.github/workflows/run-tests.yaml', '.github/actions/**', 'conda-recipe/**', 'src/**', 'genome_kit/**', 'setup.py', 'setup/**', 'tests/**') }}
+          key: gk-tarballs-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('.github/workflows/run-tests.yaml', '.github/actions/**', 'conda-recipe/**', 'src/**', 'genome_kit/**', 'setup.py', 'setup/**', 'tests/**') }}
           path: |
             ~/conda-bld
           fail-on-cache-miss: true
diff --git a/.github/workflows/publish-docs.yaml b/.github/workflows/publish-docs.yaml
index 5999bec2..435a66f0 100644
--- a/.github/workflows/publish-docs.yaml
+++ b/.github/workflows/publish-docs.yaml
@@ -40,7 +40,7 @@ jobs:
         id: restore_gk_pkg
         uses: actions/cache/restore@v4
         with:
-          key: mamba-env-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('.github/workflows/run-tests.yaml', '.github/actions/**', 'conda-recipe/**', 'src/**', 'genome_kit/**', 'setup.py', 'setup/**', 'tests/**') }}
+          key: gk-tarballs-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('.github/workflows/run-tests.yaml', '.github/actions/**', 'conda-recipe/**', 'src/**', 'genome_kit/**', 'setup.py', 'setup/**', 'tests/**') }}
           path: |
             ~/conda-bld
           fail-on-cache-miss: true
diff --git a/.github/workflows/run-tests.yaml b/.github/workflows/run-tests.yaml
index f9f31785..4ddad394 100644
--- a/.github/workflows/run-tests.yaml
+++ b/.github/workflows/run-tests.yaml
@@ -63,7 +63,7 @@ jobs:
         id: restore_gk_pkg
         uses: actions/cache/restore@v4
         with:
-          key: mamba-env-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('.github/workflows/run-tests.yaml', '.github/actions/**', 'conda-recipe/**', 'src/**', 'genome_kit/**', 'setup.py', 'setup/**', 'tests/**') }}
+          key: gk-tarballs-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('.github/workflows/run-tests.yaml', '.github/actions/**', 'conda-recipe/**', 'src/**', 'genome_kit/**', 'setup.py', 'setup/**', 'tests/**') }}
           path: |
             ~/conda-bld
           fail-on-cache-miss: true

From 5f98ce03c40ea749d3ad7bd784d512627e7f0052 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Thu, 26 Jun 2025 14:40:50 -0700
Subject: [PATCH 33/52] wip31

---
 .github/actions/build-gk/action.yaml | 10 +++++++---
 .github/workflows/run-tests.yaml     | 16 ++++++++--------
 conda-recipe/conda_build_config.yaml |  8 ++++----
 3 files changed, 19 insertions(+), 15 deletions(-)

diff --git a/.github/actions/build-gk/action.yaml b/.github/actions/build-gk/action.yaml
index 19c54101..39b2aff1 100644
--- a/.github/actions/build-gk/action.yaml
+++ b/.github/actions/build-gk/action.yaml
@@ -29,18 +29,18 @@ runs:
           ~/conda-bld
 
     - name: install mamba
+      if: ${{ steps.restore_gk_pkg.outputs.cache-hit != 'true' }}
       uses: ./.github/actions/install-mamba
       with:
         installer-url: https://micro.mamba.pm/api/micromamba/${{ inputs.platform }}/1.5.8
 
     - name: create build env
+      if: ${{ steps.restore_gk_pkg.outputs.cache-hit != 'true' }}
       shell: bash -l -e {0}
       run: |
         set -x
         if [ ! -d "${HOME}/micromamba/envs/build" ]; then
-          micromamba create -yqn build -c conda-forge \
-            boa==0.17.0 mamba==1.5.8 conda=24.5 \
-            ccache
+          micromamba create -yqn build -c conda-forge boa==0.17.0 mamba==1.5.8 conda=24.5 ccache
         fi
         set +x
 
@@ -50,6 +50,7 @@ runs:
         env: build
 
     - name: save mamba gk ccache
+      if: ${{ steps.restore_gk_pkg.outputs.cache-hit != 'true' }}
       id: save_mamba_gk_ccache
       uses: actions/cache@v4
       with:
@@ -61,6 +62,7 @@ runs:
           ~/.ccache
 
     - name: set compiler cache size
+      if: ${{ steps.restore_gk_pkg.outputs.cache-hit != 'true' }}
       shell: bash -l -e {0}
       run: |
         set -x
@@ -81,6 +83,7 @@ runs:
         conda clean -it
 
     - name: cache mamba env
+      if: ${{ steps.restore_gk_pkg.outputs.cache-hit != 'true' }}
       id: save_mamba_cache
       uses: actions/cache/save@v4
       with:
@@ -91,6 +94,7 @@ runs:
           ~/bin/micromamba
 
     - name: cache gk package tarballs
+      if: ${{ steps.restore_gk_pkg.outputs.cache-hit != 'true' }}
       id: save_gk_pkg
       uses: actions/cache/save@v4
       with:
diff --git a/.github/workflows/run-tests.yaml b/.github/workflows/run-tests.yaml
index 4ddad394..40416271 100644
--- a/.github/workflows/run-tests.yaml
+++ b/.github/workflows/run-tests.yaml
@@ -31,14 +31,14 @@ jobs:
     strategy:
       matrix:
         include:
-#          - {"pyver-short": "39", "python-version": "3.9", "platform": "linux-64", "runs-on": "ubuntu-latest"}
-#          - {"pyver-short": "39", "python-version": "3.9", "platform": "osx-64", "runs-on": "macos-latest"}
-#          - {"pyver-short": "310", "python-version": "3.10", "platform": "linux-64", "runs-on": "ubuntu-latest"}
-#          - {"pyver-short": "310", "python-version": "3.10", "platform": "osx-64", "runs-on": "macos-latest"}
-#          - {"pyver-short": "311", "python-version": "3.11", "platform": "linux-64", "runs-on": "ubuntu-latest"}
-#          - {"pyver-short": "311", "python-version": "3.11", "platform": "osx-64", "runs-on": "macos-latest"}
-#          - {"pyver-short": "312", "python-version": "3.12", "platform": "linux-64", "runs-on": "ubuntu-latest"}
-#          - {"pyver-short": "312", "python-version": "3.12", "platform": "osx-64", "runs-on": "macos-latest"}
+          - {"pyver-short": "39", "python-version": "3.9", "platform": "linux-64", "runs-on": "ubuntu-latest"}
+          - {"pyver-short": "39", "python-version": "3.9", "platform": "osx-64", "runs-on": "macos-latest"}
+          - {"pyver-short": "310", "python-version": "3.10", "platform": "linux-64", "runs-on": "ubuntu-latest"}
+          - {"pyver-short": "310", "python-version": "3.10", "platform": "osx-64", "runs-on": "macos-latest"}
+          - {"pyver-short": "311", "python-version": "3.11", "platform": "linux-64", "runs-on": "ubuntu-latest"}
+          - {"pyver-short": "311", "python-version": "3.11", "platform": "osx-64", "runs-on": "macos-latest"}
+          - {"pyver-short": "312", "python-version": "3.12", "platform": "linux-64", "runs-on": "ubuntu-latest"}
+          - {"pyver-short": "312", "python-version": "3.12", "platform": "osx-64", "runs-on": "macos-latest"}
           - {"pyver-short": "313", "python-version": "3.13", "platform": "linux-64", "runs-on": "ubuntu-latest"}
           - {"pyver-short": "313", "python-version": "3.13", "platform": "osx-64", "runs-on": "macos-latest"}
     runs-on: ${{ matrix.runs-on }}
diff --git a/conda-recipe/conda_build_config.yaml b/conda-recipe/conda_build_config.yaml
index d3682e4c..f35afa4d 100644
--- a/conda-recipe/conda_build_config.yaml
+++ b/conda-recipe/conda_build_config.yaml
@@ -7,8 +7,8 @@ c_stdlib_version:
 - '2.17' # [linux]
 - '14.5' # [osx]
 python:
-#- '3.9'
-#- '3.10'
-#- '3.11'
-#- '3.12'
+- '3.9'
+- '3.10'
+- '3.11'
+- '3.12'
 - '3.13'

From 1f8a0c7e86b3b87f601f41304c5ee994315701e5 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Thu, 26 Jun 2025 15:50:47 -0700
Subject: [PATCH 34/52] wip32

---
 .github/actions/build-gk/action.yaml | 2 +-
 .github/workflows/run-tests.yaml     | 5 +++--
 conda-recipe/meta.yaml               | 2 ++
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/actions/build-gk/action.yaml b/.github/actions/build-gk/action.yaml
index 39b2aff1..c58d4cfa 100644
--- a/.github/actions/build-gk/action.yaml
+++ b/.github/actions/build-gk/action.yaml
@@ -40,7 +40,7 @@ runs:
       run: |
         set -x
         if [ ! -d "${HOME}/micromamba/envs/build" ]; then
-          micromamba create -yqn build -c conda-forge boa==0.17.0 mamba==1.5.8 conda=24.5 ccache
+          micromamba create -yqn build -c conda-forge mamba==1.5.8 conda=24.5 ccache
         fi
         set +x
 
diff --git a/.github/workflows/run-tests.yaml b/.github/workflows/run-tests.yaml
index 40416271..47889f54 100644
--- a/.github/workflows/run-tests.yaml
+++ b/.github/workflows/run-tests.yaml
@@ -77,9 +77,10 @@ jobs:
         shell: bash -l -e {0}
         run: |
           set -x
+          # inconsistently got "coverage 7.9.1 is not supported on this platform" so removed
+          # (not needed?)
           if [ ! -d "${HOME}/micromamba/envs/test" ]; then
-            micromamba create -yqn test -c conda-forge \
-              boa==0.16.0 mamba==1.5.7 conda==24.1.2 coverage
+            micromamba create -yqn test -c conda-forge mamba==1.5.7 conda==24.1.2
           fi
           set +x
 
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 94d77955..905528b5 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -47,6 +47,8 @@ test:
   imports:
     - genome_kit
   requires:
+    # inconsistently got "coverage 7.9.1 is not supported on this platform" so removed
+    # (not needed?)
     - pip
   source_files:
     - tests

From 66041b214c7287cdc69f0fdf6490a1cdc562f74f Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Thu, 26 Jun 2025 16:39:03 -0700
Subject: [PATCH 35/52] wip33

---
 .github/actions/build-gk/action.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/actions/build-gk/action.yaml b/.github/actions/build-gk/action.yaml
index c58d4cfa..12ee8d98 100644
--- a/.github/actions/build-gk/action.yaml
+++ b/.github/actions/build-gk/action.yaml
@@ -39,8 +39,9 @@ runs:
       shell: bash -l -e {0}
       run: |
         set -x
+        # boa required for the mambabuild subcommand
         if [ ! -d "${HOME}/micromamba/envs/build" ]; then
-          micromamba create -yqn build -c conda-forge mamba==1.5.8 conda=24.5 ccache
+          micromamba create -yqn build -c conda-forge boa==0.17.0 mamba==1.5.8 conda=24.5 ccache
         fi
         set +x
 

From 35499f193923ad50fa32672f547d82879894c629 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Thu, 26 Jun 2025 16:41:24 -0700
Subject: [PATCH 36/52] wip34

---
 .github/workflows/run-tests.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/run-tests.yaml b/.github/workflows/run-tests.yaml
index 47889f54..871e24ee 100644
--- a/.github/workflows/run-tests.yaml
+++ b/.github/workflows/run-tests.yaml
@@ -76,11 +76,12 @@ jobs:
       - name: create test env
         shell: bash -l -e {0}
         run: |
+          # boa required for the mambabuild subcommand
           set -x
           # inconsistently got "coverage 7.9.1 is not supported on this platform" so removed
           # (not needed?)
           if [ ! -d "${HOME}/micromamba/envs/test" ]; then
-            micromamba create -yqn test -c conda-forge mamba==1.5.7 conda==24.1.2
+            micromamba create -yqn test -c conda-forge boa==0.16.0 mamba==1.5.7 conda==24.1.2
           fi
           set +x
 

From 1d44e584f18387478fcf0ccc3ca983b9367c1cfe Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Thu, 26 Jun 2025 18:22:01 -0700
Subject: [PATCH 37/52] wip35

---
 _pyproject.toml => pyproject.toml | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename _pyproject.toml => pyproject.toml (100%)

diff --git a/_pyproject.toml b/pyproject.toml
similarity index 100%
rename from _pyproject.toml
rename to pyproject.toml

From 2f6b1823bc5b76dc2a1347f4d61e2de339f80403 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Fri, 27 Jun 2025 07:54:47 -0700
Subject: [PATCH 38/52] wip36

---
 .github/actions/build-gk/action.yaml |   2 +
 .github/workflows/build-wheels.yaml  | 108 +++++++++++++--------------
 2 files changed, 55 insertions(+), 55 deletions(-)

diff --git a/.github/actions/build-gk/action.yaml b/.github/actions/build-gk/action.yaml
index 12ee8d98..d6656e5c 100644
--- a/.github/actions/build-gk/action.yaml
+++ b/.github/actions/build-gk/action.yaml
@@ -28,6 +28,8 @@ runs:
         path: |
           ~/conda-bld
 
+      # skip remaining steps (except configure-conda) on cache hit
+
     - name: install mamba
       if: ${{ steps.restore_gk_pkg.outputs.cache-hit != 'true' }}
       uses: ./.github/actions/install-mamba
diff --git a/.github/workflows/build-wheels.yaml b/.github/workflows/build-wheels.yaml
index 9b553a36..33ab8fa8 100644
--- a/.github/workflows/build-wheels.yaml
+++ b/.github/workflows/build-wheels.yaml
@@ -5,12 +5,14 @@ on:
   push:
     # only build+push docker on release-please tags
     tags: [ "v*" ]
+    branches:
+      - feat/py313
     paths:
     - ".github/actions/**"
     - ".github/workflows/**"
     - "genome_kit/**"
     - "setup.py"
-    - "_pyproject.toml"
+    - "pyproject.toml"
     - "setup/**"
     - "src/**"
     - "tests/**"
@@ -33,15 +35,11 @@ jobs:
         id: restore_linux_wheels
         uses: actions/cache/restore@v4
         with:
-          key: linux-wheels-${{ matrix.arch }}-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
+          key: linux-wheels-${{ matrix.arch }}-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
           path: wheelhouse/*.whl
 
       # skip remaining steps on cache hit
 
-      - if: ${{ steps.restore_linux_wheels.outputs.cache-hit != 'true' }}
-        name: Rename pyproject.toml
-        run: mv _pyproject.toml pyproject.toml
-
       - if: ${{ steps.restore_linux_wheels.outputs.cache-hit != 'true' }}
         name: Set up Python
         uses: actions/setup-python@v5
@@ -172,7 +170,7 @@ jobs:
       - name: Download built wheels
         uses: actions/cache/restore@v4
         with:
-          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
+          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
           path: wheelhouse/*.whl
           fail-on-cache-miss: true
 
@@ -214,7 +212,7 @@ jobs:
 #        id: restore_linux_intel_wheels
 #        uses: actions/cache/restore@v4
 #        with:
-#          key: linux-wheels-x86_64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
+#          key: linux-wheels-x86_64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
 #          path: wheelhouse/*.whl
 #          fail-on-cache-miss: true
 #
@@ -222,7 +220,7 @@ jobs:
 #        id: restore_linux_arm_wheels
 #        uses: actions/cache/restore@v4
 #        with:
-#          key: linux-wheels-aarch64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
+#          key: linux-wheels-aarch64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
 #          path: wheelhouse/*.whl
 #          fail-on-cache-miss: true
 #
@@ -230,7 +228,7 @@ jobs:
 #        id: restore_macos_wheels
 #        uses: actions/cache/restore@v4
 #        with:
-#          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
+#          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
 #          path: wheelhouse/*.whl
 #          fail-on-cache-miss: true
 #
@@ -248,48 +246,48 @@ jobs:
 #          verbose: 'true'
 #          skip-existing: 'true'
 
-  publish-to-pypi:
-    name: Publish to PyPI
-    needs: [build-wheel-linux, test-wheel-macos]
-    runs-on: ubuntu-latest
-
-    environment:
-      name: pypi
-      url: https://pypi.org/p/genomekit
-
-    permissions:
-      id-token: write  # mandatory for trusted publishing
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Restore the linux intel wheels cache
-        id: restore_linux_intel_wheels
-        uses: actions/cache/restore@v4
-        with:
-          key: linux-wheels-x86_64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
-          path: wheelhouse/*.whl
-          fail-on-cache-miss: true
-
-      - name: Restore the linux arm wheels cache
-        id: restore_linux_arm_wheels
-        uses: actions/cache/restore@v4
-        with:
-          key: linux-wheels-aarch64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
-          path: wheelhouse/*.whl
-          fail-on-cache-miss: true
-
-      - name: Restore the macos wheels cache
-        id: restore_macos_wheels
-        uses: actions/cache/restore@v4
-        with:
-          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
-          path: wheelhouse/*.whl
-          fail-on-cache-miss: true
-
-      - name: Publish distribution to PyPI
-        # don't use a version tag with 3rd party actions
-        uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc
-        with:
-          packages-dir: wheelhouse
-          verbose: 'true'
+#  publish-to-pypi:
+#    name: Publish to PyPI
+#    needs: [build-wheel-linux, test-wheel-macos]
+#    runs-on: ubuntu-latest
+#
+#    environment:
+#      name: pypi
+#      url: https://pypi.org/p/genomekit
+#
+#    permissions:
+#      id-token: write  # mandatory for trusted publishing
+#
+#    steps:
+#      - uses: actions/checkout@v4
+#
+#      - name: Restore the linux intel wheels cache
+#        id: restore_linux_intel_wheels
+#        uses: actions/cache/restore@v4
+#        with:
+#          key: linux-wheels-x86_64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
+#          path: wheelhouse/*.whl
+#          fail-on-cache-miss: true
+#
+#      - name: Restore the linux arm wheels cache
+#        id: restore_linux_arm_wheels
+#        uses: actions/cache/restore@v4
+#        with:
+#          key: linux-wheels-aarch64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
+#          path: wheelhouse/*.whl
+#          fail-on-cache-miss: true
+#
+#      - name: Restore the macos wheels cache
+#        id: restore_macos_wheels
+#        uses: actions/cache/restore@v4
+#        with:
+#          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
+#          path: wheelhouse/*.whl
+#          fail-on-cache-miss: true
+#
+#      - name: Publish distribution to PyPI
+#        # don't use a version tag with 3rd party actions
+#        uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc
+#        with:
+#          packages-dir: wheelhouse
+#          verbose: 'true'

From 2bc4d725b0d8d7122940fcc0291d9fa146a8cfa2 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Fri, 27 Jun 2025 10:10:05 -0700
Subject: [PATCH 39/52] wip37

---
 .github/workflows/build-wheels.yaml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/.github/workflows/build-wheels.yaml b/.github/workflows/build-wheels.yaml
index 33ab8fa8..8f8eaec8 100644
--- a/.github/workflows/build-wheels.yaml
+++ b/.github/workflows/build-wheels.yaml
@@ -104,15 +104,11 @@ jobs:
         id: restore_macos_wheels
         uses: actions/cache/restore@v4
         with:
-          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
+          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
           path: wheelhouse/*.whl
 
       # skip remaining steps on cache hit
 
-      - if: ${{ steps.restore_macos_wheels.outputs.cache-hit != 'true' }}
-        name: Rename pyproject.toml
-        run: mv _pyproject.toml pyproject.toml
-
       - if: ${{ steps.restore_macos_wheels.outputs.cache-hit != 'true' }}
         name: Set up Python
         uses: actions/setup-python@v5

From c07fb296ccc522587c9806d2e477fff96c50b479 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Fri, 27 Jun 2025 11:51:34 -0700
Subject: [PATCH 40/52] wip38

---
 .github/workflows/build-wheels.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/build-wheels.yaml b/.github/workflows/build-wheels.yaml
index 8f8eaec8..9f7efdad 100644
--- a/.github/workflows/build-wheels.yaml
+++ b/.github/workflows/build-wheels.yaml
@@ -126,6 +126,8 @@ jobs:
           GK_BUILD_WHEELS: "1"
           CIBW_ARCHS_MACOS: x86_64 arm64
           CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-* cp313-*"
+          CIBW_PIP_EXTRA_ARGS: "--no-deps --ignore-installed"
+          CIBW_ENVIRONMENT: "PYTHONPATH=."
 
       - if: ${{ steps.restore_macos_wheels.outputs.cache-hit != 'true' }}
         name: cache macos wheels

From 6e90291ea966bb266f579945c10cbf6f19affe1c Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Fri, 27 Jun 2025 14:03:22 -0700
Subject: [PATCH 41/52] wip39

---
 .github/workflows/build-wheels.yaml | 32 ++++++++++++++++++-----------
 _pyproject.toml                     |  6 ++++++
 2 files changed, 26 insertions(+), 12 deletions(-)
 create mode 100644 _pyproject.toml

diff --git a/.github/workflows/build-wheels.yaml b/.github/workflows/build-wheels.yaml
index 9f7efdad..bb2b250b 100644
--- a/.github/workflows/build-wheels.yaml
+++ b/.github/workflows/build-wheels.yaml
@@ -12,7 +12,7 @@ on:
     - ".github/workflows/**"
     - "genome_kit/**"
     - "setup.py"
-    - "pyproject.toml"
+    - "_pyproject.toml"
     - "setup/**"
     - "src/**"
     - "tests/**"
@@ -35,11 +35,15 @@ jobs:
         id: restore_linux_wheels
         uses: actions/cache/restore@v4
         with:
-          key: linux-wheels-${{ matrix.arch }}-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
+          key: linux-wheels-${{ matrix.arch }}-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
           path: wheelhouse/*.whl
 
       # skip remaining steps on cache hit
 
+      - if: ${{ steps.restore_linux_wheels.outputs.cache-hit != 'true' }}
+        name: Rename pyproject.toml
+        run: mv _pyproject.toml pyproject.toml
+
       - if: ${{ steps.restore_linux_wheels.outputs.cache-hit != 'true' }}
         name: Set up Python
         uses: actions/setup-python@v5
@@ -104,11 +108,15 @@ jobs:
         id: restore_macos_wheels
         uses: actions/cache/restore@v4
         with:
-          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
+          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
           path: wheelhouse/*.whl
 
       # skip remaining steps on cache hit
 
+      - if: ${{ steps.restore_macos_wheels.outputs.cache-hit != 'true' }}
+        name: Rename pyproject.toml
+        run: mv _pyproject.toml pyproject.toml
+
       - if: ${{ steps.restore_macos_wheels.outputs.cache-hit != 'true' }}
         name: Set up Python
         uses: actions/setup-python@v5
@@ -126,8 +134,8 @@ jobs:
           GK_BUILD_WHEELS: "1"
           CIBW_ARCHS_MACOS: x86_64 arm64
           CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-* cp313-*"
-          CIBW_PIP_EXTRA_ARGS: "--no-deps --ignore-installed"
-          CIBW_ENVIRONMENT: "PYTHONPATH=."
+#          CIBW_PIP_EXTRA_ARGS: "--no-deps --ignore-installed"
+#          CIBW_ENVIRONMENT: "PYTHONPATH=."
 
       - if: ${{ steps.restore_macos_wheels.outputs.cache-hit != 'true' }}
         name: cache macos wheels
@@ -168,7 +176,7 @@ jobs:
       - name: Download built wheels
         uses: actions/cache/restore@v4
         with:
-          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
+          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
           path: wheelhouse/*.whl
           fail-on-cache-miss: true
 
@@ -210,7 +218,7 @@ jobs:
 #        id: restore_linux_intel_wheels
 #        uses: actions/cache/restore@v4
 #        with:
-#          key: linux-wheels-x86_64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
+#          key: linux-wheels-x86_64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
 #          path: wheelhouse/*.whl
 #          fail-on-cache-miss: true
 #
@@ -218,7 +226,7 @@ jobs:
 #        id: restore_linux_arm_wheels
 #        uses: actions/cache/restore@v4
 #        with:
-#          key: linux-wheels-aarch64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
+#          key: linux-wheels-aarch64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
 #          path: wheelhouse/*.whl
 #          fail-on-cache-miss: true
 #
@@ -226,7 +234,7 @@ jobs:
 #        id: restore_macos_wheels
 #        uses: actions/cache/restore@v4
 #        with:
-#          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
+#          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
 #          path: wheelhouse/*.whl
 #          fail-on-cache-miss: true
 #
@@ -263,7 +271,7 @@ jobs:
 #        id: restore_linux_intel_wheels
 #        uses: actions/cache/restore@v4
 #        with:
-#          key: linux-wheels-x86_64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
+#          key: linux-wheels-x86_64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
 #          path: wheelhouse/*.whl
 #          fail-on-cache-miss: true
 #
@@ -271,7 +279,7 @@ jobs:
 #        id: restore_linux_arm_wheels
 #        uses: actions/cache/restore@v4
 #        with:
-#          key: linux-wheels-aarch64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
+#          key: linux-wheels-aarch64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
 #          path: wheelhouse/*.whl
 #          fail-on-cache-miss: true
 #
@@ -279,7 +287,7 @@ jobs:
 #        id: restore_macos_wheels
 #        uses: actions/cache/restore@v4
 #        with:
-#          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
+#          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
 #          path: wheelhouse/*.whl
 #          fail-on-cache-miss: true
 #
diff --git a/_pyproject.toml b/_pyproject.toml
new file mode 100644
index 00000000..ce3f3eed
--- /dev/null
+++ b/_pyproject.toml
@@ -0,0 +1,6 @@
+[build-system]
+requires = [
+    "setuptools>=61",
+    "wheel",
+    "numpy==2"
+]
\ No newline at end of file

From 638edf025e9dda599d3c0dea67d8e527c4be9020 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Fri, 27 Jun 2025 14:29:33 -0700
Subject: [PATCH 42/52] Revert "wip39"

This reverts commit 6e90291ea966bb266f579945c10cbf6f19affe1c.
---
 .github/workflows/build-wheels.yaml | 32 +++++++++++------------------
 _pyproject.toml                     |  6 ------
 2 files changed, 12 insertions(+), 26 deletions(-)
 delete mode 100644 _pyproject.toml

diff --git a/.github/workflows/build-wheels.yaml b/.github/workflows/build-wheels.yaml
index bb2b250b..9f7efdad 100644
--- a/.github/workflows/build-wheels.yaml
+++ b/.github/workflows/build-wheels.yaml
@@ -12,7 +12,7 @@ on:
     - ".github/workflows/**"
     - "genome_kit/**"
     - "setup.py"
-    - "_pyproject.toml"
+    - "pyproject.toml"
     - "setup/**"
     - "src/**"
     - "tests/**"
@@ -35,15 +35,11 @@ jobs:
         id: restore_linux_wheels
         uses: actions/cache/restore@v4
         with:
-          key: linux-wheels-${{ matrix.arch }}-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
+          key: linux-wheels-${{ matrix.arch }}-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
           path: wheelhouse/*.whl
 
       # skip remaining steps on cache hit
 
-      - if: ${{ steps.restore_linux_wheels.outputs.cache-hit != 'true' }}
-        name: Rename pyproject.toml
-        run: mv _pyproject.toml pyproject.toml
-
       - if: ${{ steps.restore_linux_wheels.outputs.cache-hit != 'true' }}
         name: Set up Python
         uses: actions/setup-python@v5
@@ -108,15 +104,11 @@ jobs:
         id: restore_macos_wheels
         uses: actions/cache/restore@v4
         with:
-          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
+          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
           path: wheelhouse/*.whl
 
       # skip remaining steps on cache hit
 
-      - if: ${{ steps.restore_macos_wheels.outputs.cache-hit != 'true' }}
-        name: Rename pyproject.toml
-        run: mv _pyproject.toml pyproject.toml
-
       - if: ${{ steps.restore_macos_wheels.outputs.cache-hit != 'true' }}
         name: Set up Python
         uses: actions/setup-python@v5
@@ -134,8 +126,8 @@ jobs:
           GK_BUILD_WHEELS: "1"
           CIBW_ARCHS_MACOS: x86_64 arm64
           CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-* cp313-*"
-#          CIBW_PIP_EXTRA_ARGS: "--no-deps --ignore-installed"
-#          CIBW_ENVIRONMENT: "PYTHONPATH=."
+          CIBW_PIP_EXTRA_ARGS: "--no-deps --ignore-installed"
+          CIBW_ENVIRONMENT: "PYTHONPATH=."
 
       - if: ${{ steps.restore_macos_wheels.outputs.cache-hit != 'true' }}
         name: cache macos wheels
@@ -176,7 +168,7 @@ jobs:
       - name: Download built wheels
         uses: actions/cache/restore@v4
         with:
-          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
+          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
           path: wheelhouse/*.whl
           fail-on-cache-miss: true
 
@@ -218,7 +210,7 @@ jobs:
 #        id: restore_linux_intel_wheels
 #        uses: actions/cache/restore@v4
 #        with:
-#          key: linux-wheels-x86_64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
+#          key: linux-wheels-x86_64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
 #          path: wheelhouse/*.whl
 #          fail-on-cache-miss: true
 #
@@ -226,7 +218,7 @@ jobs:
 #        id: restore_linux_arm_wheels
 #        uses: actions/cache/restore@v4
 #        with:
-#          key: linux-wheels-aarch64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
+#          key: linux-wheels-aarch64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
 #          path: wheelhouse/*.whl
 #          fail-on-cache-miss: true
 #
@@ -234,7 +226,7 @@ jobs:
 #        id: restore_macos_wheels
 #        uses: actions/cache/restore@v4
 #        with:
-#          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
+#          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
 #          path: wheelhouse/*.whl
 #          fail-on-cache-miss: true
 #
@@ -271,7 +263,7 @@ jobs:
 #        id: restore_linux_intel_wheels
 #        uses: actions/cache/restore@v4
 #        with:
-#          key: linux-wheels-x86_64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
+#          key: linux-wheels-x86_64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
 #          path: wheelhouse/*.whl
 #          fail-on-cache-miss: true
 #
@@ -279,7 +271,7 @@ jobs:
 #        id: restore_linux_arm_wheels
 #        uses: actions/cache/restore@v4
 #        with:
-#          key: linux-wheels-aarch64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
+#          key: linux-wheels-aarch64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
 #          path: wheelhouse/*.whl
 #          fail-on-cache-miss: true
 #
@@ -287,7 +279,7 @@ jobs:
 #        id: restore_macos_wheels
 #        uses: actions/cache/restore@v4
 #        with:
-#          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
+#          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
 #          path: wheelhouse/*.whl
 #          fail-on-cache-miss: true
 #
diff --git a/_pyproject.toml b/_pyproject.toml
deleted file mode 100644
index ce3f3eed..00000000
--- a/_pyproject.toml
+++ /dev/null
@@ -1,6 +0,0 @@
-[build-system]
-requires = [
-    "setuptools>=61",
-    "wheel",
-    "numpy==2"
-]
\ No newline at end of file

From 275fdf9652dd96fe970c8f633111827efa8d21fa Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Fri, 27 Jun 2025 14:30:02 -0700
Subject: [PATCH 43/52] wip40

---
 setup.py | 11 -----------
 1 file changed, 11 deletions(-)

diff --git a/setup.py b/setup.py
index 8abb9dd9..f9ee7c48 100644
--- a/setup.py
+++ b/setup.py
@@ -31,17 +31,6 @@ def run(self):
 
 if __name__ == "__main__":
     install_requires = []
-    if os.environ.get("GK_BUILD_WHEELS", None) is not None:
-        install_requires = [
-            "appdirs>=1.4.0",
-            "numpy<2.0dev0",
-            "google-cloud-storage>=2.10.0",
-            "boto3",
-            "tqdm",
-            "setuptools",
-            "importlib-metadata",
-            "typing-extensions",
-        ]
     setup(
         author="Deep Genomics",
         author_email="info@deepgenomics.com",

From be4acf6cc3467e146297a71268b117b35941b24d Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Wed, 2 Jul 2025 15:12:00 -0700
Subject: [PATCH 44/52] wip41

---
 setup.py       | 357 ++++++++++++++++++++++++++++++++++++++++++++++++-
 setup/c_ext.py | 352 ------------------------------------------------
 2 files changed, 354 insertions(+), 355 deletions(-)
 delete mode 100644 setup/c_ext.py

diff --git a/setup.py b/setup.py
index f9ee7c48..bd1072b5 100644
--- a/setup.py
+++ b/setup.py
@@ -1,10 +1,19 @@
 # Copyright (C) 2016-2023 Deep Genomics Inc. All Rights Reserved.
 import os
+import platform
+import sys
+import sysconfig
+from glob import glob
 from pathlib import Path
+from traceback import extract_stack
 
+from setuptools._distutils import ccompiler
+import shutil
+from setuptools import Extension
 from setuptools import setup, find_packages
+from setuptools.command.build_ext import build_ext
 from setuptools.command.egg_info import egg_info
-from setup import c_ext
+
 
 COPYRIGHT_FILE = "COPYRIGHT.txt"
 LICENSE_FILE = "LICENSE"
@@ -29,6 +38,348 @@ def run(self):
 
         egg_info.run(self)
 
+
+
+libname = "genome_kit"
+
+##############################################################
+# Define the C Extension build config
+##############################################################
+
+debug = False  # Set to True for C++ debug symbols and extra memory/bounds checks
+debug_info = debug
+debug_objects = False  # Enable printing of Python C++ instances being constructed/destructed
+toolset = "msvc" if platform.system() == "Windows" else "gcc"
+
+gen_dir = os.path.join('build', 'gen')
+include_dirs = [
+    sys.prefix + "/include",
+    gen_dir,
+    ]
+library_dirs = [sys.prefix + '/lib']
+runtime_library_dirs = []
+
+if not [x for x in extract_stack(limit=20) if 'load_setup_py_data' in x[2]]:
+    # don't load numpy if we just need the version to fill the conda-build meta.yaml template
+    import numpy as np
+    include_dirs.append(np.get_include())
+
+sources = glob("src/*.cpp")
+headers = glob("src/*.h")
+libraries = []
+
+define_macros = [
+    ("GKPY_LIBNAME", libname),
+]
+
+if debug_objects:
+    define_macros += [
+        ("GKPY_TRACE_MEM", None),  # ctor/dtor notifications from C objects
+    ]
+
+extra_compile_args = []
+extra_link_args = []
+
+if toolset == "gcc":
+    # Using multiprocessing and ccache massively speeds up incremental builds
+    ccache = shutil.which('ccache')
+    if ccache:
+        os.environ["CC"] = "{} {}".format(ccache, os.environ.get("CC", "gcc"))
+        # TODO cannot use ccache in CXX since distutils hotpatches into LDSHARED:
+        # https://github.com/python/cpython/blob/069306312addf87252e2dbf250fc7632fc8b7da3/Lib/distutils/unixccompiler.py#L191
+        os.environ["LDSHARED"] = sysconfig.get_config_var("LDSHARED")
+    else:
+        print("WARNING: did not find ccache installed; files will be built from scratch every time")
+
+    define_macros += [
+        ("_FILE_OFFSET_BITS", 64),
+    ]
+    if debug:
+        define_macros += [
+            ("GK_DEBUG", None),  # Enable debug assertions etc
+        ]
+
+    libraries += [
+        # python is not linked for conda's python
+        # https://github.com/ContinuumIO/anaconda-issues/issues/9078#issuecomment-378321357
+        "z",
+    ]
+
+    # GCC flags common to both debug and release modes
+    extra_compile_args += [
+        "-std=c++20",
+        "-fvisibility=hidden",  # reduce symbols for code size/load times
+        "-fvisibility-inlines-hidden",
+        "-Wall",
+        "-Wno-write-strings",  # char* in Python API
+        "-Wno-invalid-offsetof",  # offsetof non-POD GK types for Python API
+    ]
+
+    if debug:
+        opt_args = [
+            "-O0",
+            "-UNDEBUG",
+        ]
+    else:
+        opt_args = [
+            "-O3",
+        ]
+
+    if debug_info:
+        opt_args += [
+            "-g3",
+        ]
+    else:
+        extra_link_args += [
+            "-Wl,-S",
+            "-Wl,-x",
+        ]
+
+    if platform.system() == "Darwin":
+        # >=10.15 required for std::filesystem::remove
+        osx_sdk = "-mmacosx-version-min={}".format(os.environ.get("MACOSX_DEPLOYMENT_TARGET", "10.15"))
+
+        extra_compile_args += [
+            osx_sdk,
+            "-isysroot{}".format(os.environ.get("CONDA_BUILD_SYSROOT", "/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk")),
+            "-stdlib=libc++",
+            "-Wshorten-64-to-32",  # catch implicit truncation as per MSVC
+            "-Wsign-compare",  # match MSVC(/W3)/gcc(-Wall)
+            "-Wconditional-uninitialized",  # gcc does better here but enable for safety
+            "-Wuninitialized",
+            "-Wno-unknown-warning-option",
+        ]
+
+        extra_link_args += [
+            osx_sdk,
+            "-isysroot{}".format(os.environ.get("CONDA_BUILD_SYSROOT", "/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk")),
+        ]
+        define_macros += [
+            # https://conda-forge.org/docs/maintainer/knowledge_base/#newer-c-features-with-old-sdk
+            ("_LIBCPP_DISABLE_AVAILABILITY", None),
+        ]
+
+    extra_compile_args += opt_args
+    extra_link_args += opt_args  # required for LTO
+
+
+elif toolset == "msvc":
+
+    os.environ["DISTUTILS_USE_SDK"] = "1"
+    os.environ["MSSdk"] = "1"
+
+    condalib_dir = sys.prefix + "/Library"
+    condalib_inc = condalib_dir + "/include"
+    condalib_lib = condalib_dir + "/lib"
+    include_dirs.append(condalib_inc)
+    library_dirs.append(condalib_lib)
+
+    define_macros += [
+        ("_CRT_SECURE_NO_WARNINGS", None),
+    ]
+
+    libraries += [
+        "zlib",
+    ]
+
+    # VC flags common to both debug and release modes
+    extra_compile_args += [
+        "/std:c++20",
+        "/permissive-",
+        "/Zc:__cplusplus",
+        "/Zc:strictStrings-",  # don"t let strings be written to by default
+        # compatibility with __VA_OPT__
+        # see https://devblogs.microsoft.com/cppblog/announcing-full-support-for-a-c-c-conformant-preprocessor-in-msvc/
+        "/Zc:preprocessor",
+        "/W3",  # Warning level 3
+        "/EHsc",  # Enable C++ and structured exception handling (e.g. catch access violations)
+        "/wd5033",  # Python usage of deprecated register keyword
+    ]
+
+    extra_link_args += [
+        "/PDB:%s\\_cxx.pdb" % libname,  # Put it right beside the .pyd/.so file in "develop" mode
+    ]
+
+    if debug:
+        # do NOT define _DEBUG; need non-debug runtime to match NDEBUG Python distribution
+        # define_macros += [
+        #      ("_DEBUG", None),
+        # ]
+        extra_compile_args += [
+            "/GS",  # Enable buffer overrun checks
+            "/Zi",  # Enable debug information .pdb
+            "/Od",  # Disable optimizations
+        ]
+        extra_link_args += [
+            "/DEBUG",
+        ]
+    else:
+        extra_compile_args += [
+            "/GL",  # Enable whole-program optimization
+            "/Gy",  # Enable function-level linking
+            "/Oy",  # Omit frame pointers
+            "/Oi",  # Enable intrinsics
+            #"/Zi",  # Enable debug information .pdb
+        ]
+        extra_link_args += [
+            "/LTCG",  # Enable link-time code generation
+            #"/DEBUG",
+        ]
+
+
+class NoCWarningsBuildExt(build_ext):
+    def build_extensions(self):
+        for x in ["-Wstrict-prototypes"]:
+            try:
+                self.compiler.compiler_so.remove(x)
+            except (AttributeError, ValueError):
+                continue
+        build_ext.build_extensions(self)
+
+
+extension = Extension(
+    libname + "._cxx",
+    sources=sources,
+    depends=headers,
+    include_dirs=include_dirs,
+    define_macros=define_macros,
+    library_dirs=library_dirs,
+    libraries=libraries,
+    runtime_library_dirs=runtime_library_dirs,
+    extra_compile_args=extra_compile_args,
+    extra_link_args=extra_link_args,
+    )
+
+##############################################################
+
+# monkey-patch for parallel compilation
+# TODO
+# taken from http://stackoverflow.com/questions/11013851/speeding-up-build-process-with-distutils
+
+PARALLEL_JOBS = 4  # number of parallel compilations
+
+
+def gcc_parallel_ccompile(self,
+                          sources,
+                          output_dir=None,
+                          macros=None,
+                          include_dirs=None,
+                          debug=0,
+                          extra_preargs=None,
+                          extra_postargs=None,
+                          depends=None):
+    # those lines are copied from distutils.ccompiler.CCompiler directly
+    macros, objects, extra_postargs, pp_opts, build = self._setup_compile(output_dir, macros, include_dirs, sources,
+                                                                          depends, extra_postargs)
+    cc_args = self._get_cc_args(pp_opts, debug, extra_preargs)
+    # parallel code
+    import multiprocessing.pool
+
+    def _single_compile(obj):
+        try:
+            src, ext = build[obj]
+        except KeyError:
+            return
+        self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
+
+    # convert to list, imap is evaluated on-demand
+    list(multiprocessing.pool.ThreadPool(PARALLEL_JOBS).imap(_single_compile, objects))
+    return objects
+
+
+def windows_parallel_ccompile(self,
+                              sources,
+                              output_dir=None,
+                              macros=None,
+                              include_dirs=None,
+                              debug=0,
+                              extra_preargs=None,
+                              extra_postargs=None,
+                              depends=None):
+    if not self.initialized:
+        self.initialize()
+    compile_info = self._setup_compile(output_dir, macros, include_dirs, sources, depends, extra_postargs)
+    macros, objects, extra_postargs, pp_opts, build = compile_info
+
+    from distutils.errors import CompileError
+    from distutils.errors import DistutilsExecError
+
+    compile_opts = extra_preargs or []
+    compile_opts.append("/c")
+    compile_opts.extend(self.compile_options_debug if debug else self.compile_options)
+
+    def _compile_obj(obj):
+        try:
+            src, ext = build[obj]
+        except KeyError:
+            return
+        if debug:
+            # pass the full pathname to MSVC in debug mode,
+            # this allows the debugger to find the source file
+            # without asking the user to browse for it
+            src = os.path.abspath(src)
+
+        if ext in self._c_extensions:
+            input_opt = "/Tc" + src
+        elif ext in self._cpp_extensions:
+            input_opt = "/Tp" + src
+        elif ext in self._rc_extensions:
+            # compile .RC to .RES file
+            input_opt = src
+            output_opt = "/fo" + obj
+            try:
+                self.spawn([self.rc] + pp_opts + [output_opt] + [input_opt])
+            except DistutilsExecError as msg:
+                raise CompileError(msg)
+            return
+        elif ext in self._mc_extensions:
+            # Compile .MC to .RC file to .RES file.
+            #   * "-h dir" specifies the directory for the
+            #     generated include file
+            #   * "-r dir" specifies the target directory of the
+            #     generated RC file and the binary message resource
+            #     it includes
+            #
+            # For now (since there are no options to change this),
+            # we use the source-directory for the include file and
+            # the build directory for the RC file and message
+            # resources. This works at least for win32all.
+            h_dir = os.path.dirname(src)
+            rc_dir = os.path.dirname(obj)
+            try:
+                # first compile .MC to .RC and .H file
+                self.spawn([self.mc] + ["-h", h_dir, "-r", rc_dir] + [src])
+                base, _ = os.path.splitext(os.path.basename(src))
+                rc_file = os.path.join(rc_dir, base + ".rc")
+                # then compile .RC to .RES file
+                self.spawn([self.rc] + ["/fo" + obj] + [rc_file])
+
+            except DistutilsExecError as msg:
+                raise CompileError(msg)
+            return
+        else:
+            # how to handle this file?
+            raise CompileError("Don't know how to compile %s to %s" % (src, obj))
+
+        output_opt = "/Fo" + obj
+        try:
+            self.spawn([self.cc] + compile_opts + pp_opts + [input_opt, output_opt] + extra_postargs)
+        except DistutilsExecError as msg:
+            raise CompileError(msg)
+
+    import multiprocessing.pool
+    list(multiprocessing.pool.ThreadPool(PARALLEL_JOBS).imap(_compile_obj, objects))
+
+    return objects
+
+
+if sys.platform == "win32":
+    # TODO from setuptools._distutils._msvccompiler import MSVCCompiler
+    import distutils._msvccompiler
+    distutils._msvccompiler.MSVCCompiler.compile = windows_parallel_ccompile
+else:
+    ccompiler.CCompiler.compile = gcc_parallel_ccompile
+
 if __name__ == "__main__":
     install_requires = []
     setup(
@@ -56,10 +407,10 @@ def run(self):
             "Documentation": "https://deepgenomics.github.io/GenomeKit"
         },
         cmdclass={
-            'build_ext': c_ext.NoCWarningsBuildExt,
+            'build_ext': NoCWarningsBuildExt,
             'egg_info': egg_info_ex
         },
-        ext_modules=[c_ext.extension],
+        ext_modules=[extension],
         test_suite="tests",
         tests_require=tests_require,
         url=f"https://github.com/deepgenomics/GenomeKit",
diff --git a/setup/c_ext.py b/setup/c_ext.py
deleted file mode 100644
index 4993c6ae..00000000
--- a/setup/c_ext.py
+++ /dev/null
@@ -1,352 +0,0 @@
-# Copyright (C) 2016-2023 Deep Genomics Inc. All Rights Reserved.
-
-import os
-import platform
-import sys
-import sysconfig
-
-import distutils.ccompiler
-
-from distutils.spawn import find_executable
-from glob import glob
-from setuptools.command.build_ext import build_ext
-from setuptools import Extension
-from traceback import extract_stack
-
-libname = "genome_kit"
-
-##############################################################
-# Define the C Extension build config
-##############################################################
-
-debug = False  # Set to True for C++ debug symbols and extra memory/bounds checks
-debug_info = debug
-debug_objects = False  # Enable printing of Python C++ instances being constructed/destructed
-toolset = "msvc" if platform.system() == "Windows" else "gcc"
-
-gen_dir = os.path.join('build', 'gen')
-include_dirs = [
-    sys.prefix + "/include",
-    gen_dir,
-]
-library_dirs = [sys.prefix + '/lib']
-runtime_library_dirs = []
-
-if not [x for x in extract_stack(limit=20) if 'load_setup_py_data' in x[2]]:
-    # don't load numpy if we just need the version to fill the conda-build meta.yaml template
-    import numpy as np
-    include_dirs.append(np.get_include())
-
-sources = glob("src/*.cpp")
-headers = glob("src/*.h")
-libraries = []
-
-define_macros = [
-    ("GKPY_LIBNAME", libname),
-]
-
-if debug_objects:
-    define_macros += [
-        ("GKPY_TRACE_MEM", None),  # ctor/dtor notifications from C objects
-    ]
-
-extra_compile_args = []
-extra_link_args = []
-
-if toolset == "gcc":
-    # Using multiprocessing and ccache massively speeds up incremental builds
-    ccache = find_executable('ccache')
-    if ccache:
-        os.environ["CC"] = "{} {}".format(ccache, os.environ.get("CC", "gcc"))
-        # cannot use ccache in CXX since distutils hotpatches into LDSHARED:
-        # https://github.com/python/cpython/blob/069306312addf87252e2dbf250fc7632fc8b7da3/Lib/distutils/unixccompiler.py#L191
-        os.environ["LDSHARED"] = sysconfig.get_config_var("LDSHARED")
-    else:
-        print("WARNING: did not find ccache installed; files will be built from scratch every time")
-
-    define_macros += [
-        ("_FILE_OFFSET_BITS", 64),
-    ]
-    if debug:
-        define_macros += [
-            ("GK_DEBUG", None),  # Enable debug assertions etc
-        ]
-
-    libraries += [
-        # python is not linked for conda's python
-        # https://github.com/ContinuumIO/anaconda-issues/issues/9078#issuecomment-378321357
-        "z",
-    ]
-
-    # GCC flags common to both debug and release modes
-    extra_compile_args += [
-        "-std=c++20",
-        "-fvisibility=hidden",  # reduce symbols for code size/load times
-        "-fvisibility-inlines-hidden",
-        "-Wall",
-        "-Wno-write-strings",  # char* in Python API
-        "-Wno-invalid-offsetof",  # offsetof non-POD GK types for Python API
-    ]
-
-    if debug:
-        opt_args = [
-            "-O0",
-            "-UNDEBUG",
-        ]
-    else:
-        opt_args = [
-            "-O3",
-        ]
-
-    if debug_info:
-        opt_args += [
-            "-g3",
-        ]
-    else:
-        extra_link_args += [
-            "-Wl,-S",
-            "-Wl,-x",
-        ]
-
-    if platform.system() == "Darwin":
-        # >=10.15 required for std::filesystem::remove
-        osx_sdk = "-mmacosx-version-min={}".format(os.environ.get("MACOSX_DEPLOYMENT_TARGET", "10.15"))
-
-        extra_compile_args += [
-            osx_sdk,
-            "-isysroot{}".format(os.environ.get("CONDA_BUILD_SYSROOT", "/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk")),
-            "-stdlib=libc++",
-            "-Wshorten-64-to-32",  # catch implicit truncation as per MSVC
-            "-Wsign-compare",  # match MSVC(/W3)/gcc(-Wall)
-            "-Wconditional-uninitialized",  # gcc does better here but enable for safety
-            "-Wuninitialized",
-            "-Wno-unknown-warning-option",
-        ]
-
-        extra_link_args += [
-            osx_sdk,
-            "-isysroot{}".format(os.environ.get("CONDA_BUILD_SYSROOT", "/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk")),
-        ]
-        define_macros += [
-            # https://conda-forge.org/docs/maintainer/knowledge_base/#newer-c-features-with-old-sdk
-            ("_LIBCPP_DISABLE_AVAILABILITY", None),
-        ]
-
-    extra_compile_args += opt_args
-    extra_link_args += opt_args  # required for LTO
-
-
-elif toolset == "msvc":
-
-    os.environ["DISTUTILS_USE_SDK"] = "1"
-    os.environ["MSSdk"] = "1"
-
-    condalib_dir = sys.prefix + "/Library"
-    condalib_inc = condalib_dir + "/include"
-    condalib_lib = condalib_dir + "/lib"
-    include_dirs.append(condalib_inc)
-    library_dirs.append(condalib_lib)
-
-    define_macros += [
-        ("_CRT_SECURE_NO_WARNINGS", None),
-    ]
-
-    libraries += [
-        "zlib",
-    ]
-
-    # VC flags common to both debug and release modes
-    extra_compile_args += [
-        "/std:c++20",
-        "/permissive-",
-        "/Zc:__cplusplus",
-        "/Zc:strictStrings-",  # don"t let strings be written to by default
-        # compatibility with __VA_OPT__
-        # see https://devblogs.microsoft.com/cppblog/announcing-full-support-for-a-c-c-conformant-preprocessor-in-msvc/
-        "/Zc:preprocessor",
-        "/W3",  # Warning level 3
-        "/EHsc",  # Enable C++ and structured exception handling (e.g. catch access violations)
-        "/wd5033",  # Python usage of deprecated register keyword
-    ]
-
-    extra_link_args += [
-        "/PDB:%s\\_cxx.pdb" % libname,  # Put it right beside the .pyd/.so file in "develop" mode
-    ]
-
-    if debug:
-        # do NOT define _DEBUG; need non-debug runtime to match NDEBUG Python distribution
-        # define_macros += [
-        #      ("_DEBUG", None),
-        # ]
-        extra_compile_args += [
-            "/GS",  # Enable buffer overrun checks
-            "/Zi",  # Enable debug information .pdb
-            "/Od",  # Disable optimizations
-        ]
-        extra_link_args += [
-            "/DEBUG",
-        ]
-    else:
-        extra_compile_args += [
-            "/GL",  # Enable whole-program optimization
-            "/Gy",  # Enable function-level linking
-            "/Oy",  # Omit frame pointers
-            "/Oi",  # Enable intrinsics
-            #"/Zi",  # Enable debug information .pdb
-        ]
-        extra_link_args += [
-            "/LTCG",  # Enable link-time code generation
-            #"/DEBUG",
-        ]
-
-
-class NoCWarningsBuildExt(build_ext):
-    def build_extensions(self):
-        for x in ["-Wstrict-prototypes"]:
-            try:
-                self.compiler.compiler_so.remove(x)
-            except (AttributeError, ValueError):
-                continue
-        build_ext.build_extensions(self)
-
-
-extension = Extension(
-    libname + "._cxx",
-    sources=sources,
-    depends=headers,
-    include_dirs=include_dirs,
-    define_macros=define_macros,
-    library_dirs=library_dirs,
-    libraries=libraries,
-    runtime_library_dirs=runtime_library_dirs,
-    extra_compile_args=extra_compile_args,
-    extra_link_args=extra_link_args,
-)
-
-##############################################################
-
-# monkey-patch for parallel compilation
-# taken from http://stackoverflow.com/questions/11013851/speeding-up-build-process-with-distutils
-
-PARALLEL_JOBS = 4  # number of parallel compilations
-
-
-def gcc_parallel_ccompile(self,
-                          sources,
-                          output_dir=None,
-                          macros=None,
-                          include_dirs=None,
-                          debug=0,
-                          extra_preargs=None,
-                          extra_postargs=None,
-                          depends=None):
-    # those lines are copied from distutils.ccompiler.CCompiler directly
-    macros, objects, extra_postargs, pp_opts, build = self._setup_compile(output_dir, macros, include_dirs, sources,
-                                                                          depends, extra_postargs)
-    cc_args = self._get_cc_args(pp_opts, debug, extra_preargs)
-    # parallel code
-    import multiprocessing.pool
-
-    def _single_compile(obj):
-        try:
-            src, ext = build[obj]
-        except KeyError:
-            return
-        self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
-
-    # convert to list, imap is evaluated on-demand
-    list(multiprocessing.pool.ThreadPool(PARALLEL_JOBS).imap(_single_compile, objects))
-    return objects
-
-
-def windows_parallel_ccompile(self,
-                              sources,
-                              output_dir=None,
-                              macros=None,
-                              include_dirs=None,
-                              debug=0,
-                              extra_preargs=None,
-                              extra_postargs=None,
-                              depends=None):
-    if not self.initialized:
-        self.initialize()
-    compile_info = self._setup_compile(output_dir, macros, include_dirs, sources, depends, extra_postargs)
-    macros, objects, extra_postargs, pp_opts, build = compile_info
-
-    from distutils.errors import CompileError
-    from distutils.errors import DistutilsExecError
-
-    compile_opts = extra_preargs or []
-    compile_opts.append("/c")
-    compile_opts.extend(self.compile_options_debug if debug else self.compile_options)
-
-    def _compile_obj(obj):
-        try:
-            src, ext = build[obj]
-        except KeyError:
-            return
-        if debug:
-            # pass the full pathname to MSVC in debug mode,
-            # this allows the debugger to find the source file
-            # without asking the user to browse for it
-            src = os.path.abspath(src)
-
-        if ext in self._c_extensions:
-            input_opt = "/Tc" + src
-        elif ext in self._cpp_extensions:
-            input_opt = "/Tp" + src
-        elif ext in self._rc_extensions:
-            # compile .RC to .RES file
-            input_opt = src
-            output_opt = "/fo" + obj
-            try:
-                self.spawn([self.rc] + pp_opts + [output_opt] + [input_opt])
-            except DistutilsExecError as msg:
-                raise CompileError(msg)
-            return
-        elif ext in self._mc_extensions:
-            # Compile .MC to .RC file to .RES file.
-            #   * "-h dir" specifies the directory for the
-            #     generated include file
-            #   * "-r dir" specifies the target directory of the
-            #     generated RC file and the binary message resource
-            #     it includes
-            #
-            # For now (since there are no options to change this),
-            # we use the source-directory for the include file and
-            # the build directory for the RC file and message
-            # resources. This works at least for win32all.
-            h_dir = os.path.dirname(src)
-            rc_dir = os.path.dirname(obj)
-            try:
-                # first compile .MC to .RC and .H file
-                self.spawn([self.mc] + ["-h", h_dir, "-r", rc_dir] + [src])
-                base, _ = os.path.splitext(os.path.basename(src))
-                rc_file = os.path.join(rc_dir, base + ".rc")
-                # then compile .RC to .RES file
-                self.spawn([self.rc] + ["/fo" + obj] + [rc_file])
-
-            except DistutilsExecError as msg:
-                raise CompileError(msg)
-            return
-        else:
-            # how to handle this file?
-            raise CompileError("Don't know how to compile %s to %s" % (src, obj))
-
-        output_opt = "/Fo" + obj
-        try:
-            self.spawn([self.cc] + compile_opts + pp_opts + [input_opt, output_opt] + extra_postargs)
-        except DistutilsExecError as msg:
-            raise CompileError(msg)
-
-    import multiprocessing.pool
-    list(multiprocessing.pool.ThreadPool(PARALLEL_JOBS).imap(_compile_obj, objects))
-
-    return objects
-
-
-if sys.platform == "win32":
-    import distutils._msvccompiler
-    distutils._msvccompiler.MSVCCompiler.compile = windows_parallel_ccompile
-else:
-    distutils.ccompiler.CCompiler.compile = gcc_parallel_ccompile

From 7c94ba71328b9f74a9c2dff6189d0e2f69a53002 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Wed, 2 Jul 2025 15:37:18 -0700
Subject: [PATCH 45/52] wip42

---
 .github/actions/curl-meta-yaml/action.yaml |  3 ++-
 .github/workflows/build-wheels.yaml        |  2 --
 setup.py                                   | 12 ++++++++++++
 3 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/.github/actions/curl-meta-yaml/action.yaml b/.github/actions/curl-meta-yaml/action.yaml
index f0666a5e..1f40e81d 100644
--- a/.github/actions/curl-meta-yaml/action.yaml
+++ b/.github/actions/curl-meta-yaml/action.yaml
@@ -38,7 +38,8 @@ runs:
         # set the version to the local release-please version (for docs and docker publish)
         $SED_CMD "s/{% set version = \".+\" %}/{% set version = \"${GK_VERSION}\" %}/" conda-recipe/meta.yaml
         # avoid error "No module named 'setup'" due to "from setup import c_ext" in setup.py
-        $SED_CMD "s/script: {{ PYTHON }} -m pip install --no-deps --ignore-installed ./script: PYTHONPATH=. {{ PYTHON }} -m pip install --no-deps --ignore-installed ./" conda-recipe/meta.yaml
+        # See if this can be removed
+        # $SED_CMD "s/script: {{ PYTHON }} -m pip install --no-deps --ignore-installed ./script: PYTHONPATH=. {{ PYTHON }} -m pip install --no-deps --ignore-installed ./" conda-recipe/meta.yaml
 
         head -40 conda-recipe/meta.yaml
         set +x
diff --git a/.github/workflows/build-wheels.yaml b/.github/workflows/build-wheels.yaml
index 9f7efdad..8f8eaec8 100644
--- a/.github/workflows/build-wheels.yaml
+++ b/.github/workflows/build-wheels.yaml
@@ -126,8 +126,6 @@ jobs:
           GK_BUILD_WHEELS: "1"
           CIBW_ARCHS_MACOS: x86_64 arm64
           CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-* cp313-*"
-          CIBW_PIP_EXTRA_ARGS: "--no-deps --ignore-installed"
-          CIBW_ENVIRONMENT: "PYTHONPATH=."
 
       - if: ${{ steps.restore_macos_wheels.outputs.cache-hit != 'true' }}
         name: cache macos wheels
diff --git a/setup.py b/setup.py
index bd1072b5..9f8ff1b0 100644
--- a/setup.py
+++ b/setup.py
@@ -382,6 +382,18 @@ def _compile_obj(obj):
 
 if __name__ == "__main__":
     install_requires = []
+    if os.environ.get("GK_BUILD_WHEELS", None) is not None:
+        install_requires = [
+            "appdirs>=1.4.0",
+            "numpy=2; python_version>='3.13'",
+            "numpy<2.0dev0; python_version<'3.13'"
+            "google-cloud-storage>=2.10.0",
+            "boto3",
+            "tqdm",
+            "setuptools",
+            "importlib-metadata",
+            "typing-extensions",
+        ]
     setup(
         author="Deep Genomics",
         author_email="info@deepgenomics.com",

From 2c840b67aa1fad99ddc0773a446c03d2f810f42e Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Wed, 2 Jul 2025 15:45:55 -0700
Subject: [PATCH 46/52] wip43

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 9f8ff1b0..df98c02f 100644
--- a/setup.py
+++ b/setup.py
@@ -385,7 +385,7 @@ def _compile_obj(obj):
     if os.environ.get("GK_BUILD_WHEELS", None) is not None:
         install_requires = [
             "appdirs>=1.4.0",
-            "numpy=2; python_version>='3.13'",
+            "numpy>=2.0.0; python_version>='3.13'",
             "numpy<2.0dev0; python_version<'3.13'"
             "google-cloud-storage>=2.10.0",
             "boto3",

From f540e1e18290f989ed589246e35e262080c59a51 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Wed, 2 Jul 2025 15:50:32 -0700
Subject: [PATCH 47/52] wip44

---
 setup.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index df98c02f..48726c54 100644
--- a/setup.py
+++ b/setup.py
@@ -385,8 +385,8 @@ def _compile_obj(obj):
     if os.environ.get("GK_BUILD_WHEELS", None) is not None:
         install_requires = [
             "appdirs>=1.4.0",
-            "numpy>=2.0.0; python_version>='3.13'",
-            "numpy<2.0dev0; python_version<'3.13'"
+            "numpy=2; python_version>='3.13'",
+            "numpy<2.0dev0; python_version<'3.13'",
             "google-cloud-storage>=2.10.0",
             "boto3",
             "tqdm",

From 00c86019efe33720ed1d60e1ad01923295862a87 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Wed, 2 Jul 2025 15:53:33 -0700
Subject: [PATCH 48/52] wip45

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 48726c54..b4871033 100644
--- a/setup.py
+++ b/setup.py
@@ -385,7 +385,7 @@ def _compile_obj(obj):
     if os.environ.get("GK_BUILD_WHEELS", None) is not None:
         install_requires = [
             "appdirs>=1.4.0",
-            "numpy=2; python_version>='3.13'",
+            "numpy=>2.0.0; python_version>='3.13'",
             "numpy<2.0dev0; python_version<'3.13'",
             "google-cloud-storage>=2.10.0",
             "boto3",

From 09ed3a867cc2ce7fff695232e7351dc7928e64c9 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Wed, 2 Jul 2025 16:02:51 -0700
Subject: [PATCH 49/52] wip46

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index b4871033..55e93ee3 100644
--- a/setup.py
+++ b/setup.py
@@ -385,7 +385,7 @@ def _compile_obj(obj):
     if os.environ.get("GK_BUILD_WHEELS", None) is not None:
         install_requires = [
             "appdirs>=1.4.0",
-            "numpy=>2.0.0; python_version>='3.13'",
+            "numpy>=2.0.0; python_version>='3.13'",
             "numpy<2.0dev0; python_version<'3.13'",
             "google-cloud-storage>=2.10.0",
             "boto3",

From 0e1f3b70e2a1153a8accf8c6537d64905382700c Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Wed, 2 Jul 2025 16:26:59 -0700
Subject: [PATCH 50/52] wip47

---
 .github/workflows/build-wheels.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-wheels.yaml b/.github/workflows/build-wheels.yaml
index 8f8eaec8..4e06dff8 100644
--- a/.github/workflows/build-wheels.yaml
+++ b/.github/workflows/build-wheels.yaml
@@ -124,7 +124,7 @@ jobs:
         run: python -m cibuildwheel --output-dir wheelhouse && ls -l wheelhouse/
         env:
           GK_BUILD_WHEELS: "1"
-          CIBW_ARCHS_MACOS: x86_64 arm64
+          CIBW_ARCHS_MACOS: arm64
           CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-* cp313-*"
 
       - if: ${{ steps.restore_macos_wheels.outputs.cache-hit != 'true' }}

From c802ec750652f9f298b72aa1c96ee3746ebdc13f Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Wed, 2 Jul 2025 21:07:36 -0700
Subject: [PATCH 51/52] wip48

---
 .github/workflows/build-wheels.yaml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build-wheels.yaml b/.github/workflows/build-wheels.yaml
index 4e06dff8..29c3a527 100644
--- a/.github/workflows/build-wheels.yaml
+++ b/.github/workflows/build-wheels.yaml
@@ -124,8 +124,8 @@ jobs:
         run: python -m cibuildwheel --output-dir wheelhouse && ls -l wheelhouse/
         env:
           GK_BUILD_WHEELS: "1"
-          CIBW_ARCHS_MACOS: arm64
-          CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-* cp313-*"
+          CIBW_ARCHS_MACOS: x86_64 arm64
+          CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-* cp313-arm64"
 
       - if: ${{ steps.restore_macos_wheels.outputs.cache-hit != 'true' }}
         name: cache macos wheels
@@ -153,7 +153,6 @@ jobs:
           - {"os": "macos-13", "arch": "x86_64", "pyver": "3.10", "pyvershort": "310"}
           - {"os": "macos-13", "arch": "x86_64", "pyver": "3.11", "pyvershort": "311"}
           - {"os": "macos-13", "arch": "x86_64", "pyver": "3.12", "pyvershort": "312"}
-          - {"os": "macos-13", "arch": "x86_64", "pyver": "3.13", "pyvershort": "313"}
 
     steps:
       - name: Set up Python

From 92634d7074c4cf7997a568b4418e07c08ee1e761 Mon Sep 17 00:00:00 2001
From: Avishai Weissberg <avishai@deepgenomics.com>
Date: Wed, 2 Jul 2025 21:30:50 -0700
Subject: [PATCH 52/52] wip49

---
 .github/workflows/build-wheels.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-wheels.yaml b/.github/workflows/build-wheels.yaml
index 29c3a527..d54db929 100644
--- a/.github/workflows/build-wheels.yaml
+++ b/.github/workflows/build-wheels.yaml
@@ -125,7 +125,7 @@ jobs:
         env:
           GK_BUILD_WHEELS: "1"
           CIBW_ARCHS_MACOS: x86_64 arm64
-          CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-* cp313-arm64"
+          CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-* cp313-macosx_arm64"
 
       - if: ${{ steps.restore_macos_wheels.outputs.cache-hit != 'true' }}
         name: cache macos wheels