From 0f47bf70c50e366de793b597ae30e899510de565 Mon Sep 17 00:00:00 2001
From: Jeroen Dries <jeroen.dries@vito.be>
Date: Wed, 25 Mar 2026 07:22:58 +0100
Subject: [PATCH 01/23] use newer numpy & python

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index d650f55..34bcffc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools>=42", "wheel", "numpy==1.23.5"]
+requires = ["setuptools>=42", "wheel", "numpy>=2.0"]
 build-backend = "setuptools.build_meta"
 
 [tool.black]
@@ -7,7 +7,7 @@ line-length = 120
 
 [tool.ruff]
 line-length = 120
-target-version = "py38"
+target-version = "py311"
 select = ["F401", "I"]
 fix = true
 

From 8d736455c52914ce5707676667a298de1d33996c Mon Sep 17 00:00:00 2001
From: Jeroen Dries <jeroen.dries@vito.be>
Date: Wed, 25 Mar 2026 08:19:39 +0100
Subject: [PATCH 02/23] fix h5py dep

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

diff --git a/setup.cfg b/setup.cfg
index 2ac5ef6..c0bef70 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -41,7 +41,7 @@ dev =
     pre-commit
     sphinx>=4.5.0
     myst-parser>=0.17.0
-    h5netcdf
+    h5netcdf[h5py]
     sphinx-autodoc-annotation
     sphinx-autodoc-typehints
     sphinxcontrib-svg2pdfconverter==1.2.0

From cbc192703d224e4621735abf806e10587acdf219 Mon Sep 17 00:00:00 2001
From: Jeroen Dries <jeroen.dries@vito.be>
Date: Wed, 25 Mar 2026 08:34:19 +0100
Subject: [PATCH 03/23] Update numpy

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

diff --git a/setup.cfg b/setup.cfg
index c0bef70..077a37e 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -21,7 +21,7 @@ package_dir =
 packages = find:
 python_requires = >= 3.8
 install_requires =
-    numpy==1.23.5
+    numpy>=2.0
     GPy>=1.10.0
     vam.whittaker==2.0.6
     # Workaround for missing GPy dependency (https://github.com/SheffieldML/GPy/issues/980)

From 8305c3ea1699943e4778303158d877dd19d1475d Mon Sep 17 00:00:00 2001
From: Jeroen Dries <jeroen.dries@vito.be>
Date: Wed, 25 Mar 2026 10:54:16 +0100
Subject: [PATCH 04/23] make scipy explicit

---
 setup.cfg | 1 +
 1 file changed, 1 insertion(+)

diff --git a/setup.cfg b/setup.cfg
index 077a37e..647186d 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -22,6 +22,7 @@ packages = find:
 python_requires = >= 3.8
 install_requires =
     numpy>=2.0
+    scipy>=1.10.0
     GPy>=1.10.0
     vam.whittaker==2.0.6
     # Workaround for missing GPy dependency (https://github.com/SheffieldML/GPy/issues/980)

From 4b4917f6eee3ed99baaa4b7032d62cbc18e46930 Mon Sep 17 00:00:00 2001
From: Jeroen Dries <jeroen.dries@vito.be>
Date: Wed, 25 Mar 2026 11:27:05 +0100
Subject: [PATCH 05/23] Update matplotlib: force lengthy dependency resolution

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

diff --git a/setup.cfg b/setup.cfg
index 647186d..a292d9e 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -26,7 +26,7 @@ install_requires =
     GPy>=1.10.0
     vam.whittaker==2.0.6
     # Workaround for missing GPy dependency (https://github.com/SheffieldML/GPy/issues/980)
-    matplotlib>=3.3.4
+    matplotlib>=3.9.0
     xarray>=0.20.2
     lcmap-pyccd==2021.7.19
     openeo

From b923bfc38868f878c751f270d8b3ae946a0c3d55 Mon Sep 17 00:00:00 2001
From: Jeroen Dries <jeroen.dries@vito.be>
Date: Wed, 25 Mar 2026 11:34:59 +0100
Subject: [PATCH 06/23] use uv for faster deps

---
 Jenkinsfile | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/Jenkinsfile b/Jenkinsfile
index 625d1e4..1be6ff9 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -13,4 +13,6 @@ pythonPipeline {
   wheel_repo = 'python-openeo'
   wheel_repo_dev = 'python-openeo'
   pep440 = true
+  enable_caching = true
+  enable_uv = true
 }

From 89b6342032434c62ca7384f6ba072c29410f2e7e Mon Sep 17 00:00:00 2001
From: Jeroen Dries <jeroen.dries@vito.be>
Date: Thu, 7 May 2026 16:13:48 +0200
Subject: [PATCH 07/23] update python version in gh actions

---
 .github/workflows/lint-and-test.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/lint-and-test.yml b/.github/workflows/lint-and-test.yml
index 8ad41ce..5a0ee0b 100644
--- a/.github/workflows/lint-and-test.yml
+++ b/.github/workflows/lint-and-test.yml
@@ -17,7 +17,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.8"
+          python-version: "3.11"
 
       - uses: pre-commit/action@v3.0.0
         with:
@@ -27,7 +27,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.8", "3.9", "3.10" ]
+        python-version: [ "3.11", "3.12" ]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -50,4 +50,4 @@ jobs:
           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
       - name: Test with pytest
         run: |
-          pytest
\ No newline at end of file
+          pytest

From 286321c3a7d54ea091d06521f6ab2805f881f180 Mon Sep 17 00:00:00 2001
From: Jeroen Dries <jeroen.dries@vito.be>
Date: Fri, 8 May 2026 08:01:49 +0200
Subject: [PATCH 08/23] remove workarounds

---
 .github/workflows/lint-and-test.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/lint-and-test.yml b/.github/workflows/lint-and-test.yml
index 5a0ee0b..447b5a8 100644
--- a/.github/workflows/lint-and-test.yml
+++ b/.github/workflows/lint-and-test.yml
@@ -36,11 +36,9 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
-          # Keep pip below 23.0.1 (vam.whittaker install fails with higher versions, #84)
-          python -m pip install --upgrade 'pip<23.0.1'
+          python -m pip install --upgrade 
           pip install flake8 pytest
-          # Workaround for vam.whittaker installation issue https://github.com/WFP-VAM/vam.whittaker/issues/4
-          pip install numpy==1.23.5 cython
+          pip install cython
           pip install .[dev]
       - name: Lint with flake8
         run: |

From 7a593aca5aaba28bfde9c2a1c7284e035da46f39 Mon Sep 17 00:00:00 2001
From: Jeroen Dries <jeroen.dries@vito.be>
Date: Fri, 8 May 2026 08:06:09 +0200
Subject: [PATCH 09/23] add location for custom package builds

---
 .github/workflows/lint-and-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/lint-and-test.yml b/.github/workflows/lint-and-test.yml
index 447b5a8..2ebd820 100644
--- a/.github/workflows/lint-and-test.yml
+++ b/.github/workflows/lint-and-test.yml
@@ -39,7 +39,7 @@ jobs:
           python -m pip install --upgrade 
           pip install flake8 pytest
           pip install cython
-          pip install .[dev]
+          pip install .[dev] --extra-index-url https://artifactory.vgt.vito.be/artifactory/api/pypi/python-packages-public/simple
       - name: Lint with flake8
         run: |
           # stop the build if there are Python syntax errors or undefined names

From ea1962a073b4d3ce39dc40349590e4bb1b4fd4d3 Mon Sep 17 00:00:00 2001
From: Jeroen Dries <jeroen.dries@vito.be>
Date: Fri, 8 May 2026 08:08:04 +0200
Subject: [PATCH 10/23] fixup

---
 .github/workflows/lint-and-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/lint-and-test.yml b/.github/workflows/lint-and-test.yml
index 2ebd820..68cfc40 100644
--- a/.github/workflows/lint-and-test.yml
+++ b/.github/workflows/lint-and-test.yml
@@ -36,7 +36,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade 
+          python -m pip install --upgrade pip
           pip install flake8 pytest
           pip install cython
           pip install .[dev] --extra-index-url https://artifactory.vgt.vito.be/artifactory/api/pypi/python-packages-public/simple

From 0fa52354c87c91472a810cfff16c78b4bffd0c98 Mon Sep 17 00:00:00 2001
From: Jeroen Dries <jeroen.dries@vito.be>
Date: Fri, 8 May 2026 08:20:53 +0200
Subject: [PATCH 11/23] scipy can be higher version

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

diff --git a/setup.cfg b/setup.cfg
index a292d9e..beefad5 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -22,7 +22,7 @@ packages = find:
 python_requires = >= 3.8
 install_requires =
     numpy>=2.0
-    scipy>=1.10.0
+    scipy
     GPy>=1.10.0
     vam.whittaker==2.0.6
     # Workaround for missing GPy dependency (https://github.com/SheffieldML/GPy/issues/980)

From 9665e449395d2718b1984d522e50a80407f2ed38 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 8 May 2026 06:28:38 +0000
Subject: [PATCH 12/23] ci: install openblas for scipy builds

Agent-Logs-Url: https://github.com/Open-EO/FuseTS/sessions/87f477a5-ea9d-4875-9c1b-af5c354daf92

Co-authored-by: jdries <5937096+jdries@users.noreply.github.com>
---
 .github/workflows/lint-and-test.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/lint-and-test.yml b/.github/workflows/lint-and-test.yml
index 68cfc40..a769d3d 100644
--- a/.github/workflows/lint-and-test.yml
+++ b/.github/workflows/lint-and-test.yml
@@ -36,6 +36,8 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
+          sudo apt-get update
+          sudo apt-get install --yes libopenblas-dev
           python -m pip install --upgrade pip
           pip install flake8 pytest
           pip install cython

From 9c57c56de5ae3f926848664c27f8f49cc6cba63f Mon Sep 17 00:00:00 2001
From: Jeroen Dries <jeroen.dries@vito.be>
Date: Fri, 8 May 2026 09:04:34 +0200
Subject: [PATCH 13/23] force specific whittaker without libc issue

---
 setup.cfg | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 1225cb2..cf9bf29 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -22,7 +22,9 @@ packages = find:
 python_requires = >= 3.8
 install_requires =
     numpy>=2.0
-    vam.whittaker==2.0.6
+    vam.whittaker@https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp311-cp311-linux_x86_64.whl; python_version == "3.11" and sys_platform == "linux"
+    vam.whittaker@https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp312-cp312-linux_x86_64.whl; python_version == "3.12" and sys_platform == "linux"
+    vam.whittaker; sys_platform == "windows"
     xarray>=0.20.2
     lcmap-pyccd==2021.7.19
     openeo

From 95831f6c2ca849c3f5e674211154f084b68971ef Mon Sep 17 00:00:00 2001
From: Jeroen Dries <jeroen.dries@vito.be>
Date: Fri, 8 May 2026 11:33:23 +0200
Subject: [PATCH 14/23] fixup

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

diff --git a/setup.cfg b/setup.cfg
index cf9bf29..22beec5 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -22,8 +22,8 @@ packages = find:
 python_requires = >= 3.8
 install_requires =
     numpy>=2.0
-    vam.whittaker@https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp311-cp311-linux_x86_64.whl; python_version == "3.11" and sys_platform == "linux"
-    vam.whittaker@https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp312-cp312-linux_x86_64.whl; python_version == "3.12" and sys_platform == "linux"
+    vam.whittaker@https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp311-cp311-linux_x86_64.whl; python_version == "3.11" and sys_platform == "linux",
+    vam.whittaker@https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp312-cp312-linux_x86_64.whl; python_version == "3.12" and sys_platform == "linux",
     vam.whittaker; sys_platform == "windows"
     xarray>=0.20.2
     lcmap-pyccd==2021.7.19

From b58f3051c6d6030c71af92dc12c13b694c918aec Mon Sep 17 00:00:00 2001
From: Jeroen Dries <jeroen.dries@vito.be>
Date: Fri, 8 May 2026 11:37:09 +0200
Subject: [PATCH 15/23] fixup

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

diff --git a/setup.cfg b/setup.cfg
index 22beec5..62fe0ce 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -22,8 +22,8 @@ packages = find:
 python_requires = >= 3.8
 install_requires =
     numpy>=2.0
-    vam.whittaker@https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp311-cp311-linux_x86_64.whl; python_version == "3.11" and sys_platform == "linux",
-    vam.whittaker@https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp312-cp312-linux_x86_64.whl; python_version == "3.12" and sys_platform == "linux",
+    'vam.whittaker@https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp311-cp311-linux_x86_64.whl; python_version == "3.11" and sys_platform == "linux"',
+    'vam.whittaker@https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp312-cp312-linux_x86_64.whl; python_version == "3.12" and sys_platform == "linux"',
     vam.whittaker; sys_platform == "windows"
     xarray>=0.20.2
     lcmap-pyccd==2021.7.19

From 40fa2f1017d14d352fa1baabff8534f5b481243c Mon Sep 17 00:00:00 2001
From: Jeroen Dries <jeroen.dries@vito.be>
Date: Fri, 8 May 2026 11:45:19 +0200
Subject: [PATCH 16/23] fixup

---
 setup.cfg | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index 62fe0ce..273c7c9 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -22,9 +22,9 @@ packages = find:
 python_requires = >= 3.8
 install_requires =
     numpy>=2.0
-    'vam.whittaker@https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp311-cp311-linux_x86_64.whl; python_version == "3.11" and sys_platform == "linux"',
-    'vam.whittaker@https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp312-cp312-linux_x86_64.whl; python_version == "3.12" and sys_platform == "linux"',
-    vam.whittaker; sys_platform == "windows"
+    'vam_whittaker@https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp311-cp311-linux_x86_64.whl; python_version=="3.11" and sys_platform=="linux"',
+    'vam_whittaker@https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp312-cp312-linux_x86_64.whl; python_version=="3.12" and sys_platform=="linux"',
+    vam_whittaker; sys_platform=="windows"
     xarray>=0.20.2
     lcmap-pyccd==2021.7.19
     openeo

From 343c17d0e015aa7b7e11a5df6d6686b0d5a665e5 Mon Sep 17 00:00:00 2001
From: Jeroen Dries <jeroen.dries@vito.be>
Date: Fri, 8 May 2026 11:55:00 +0200
Subject: [PATCH 17/23] better dep spec

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

diff --git a/setup.cfg b/setup.cfg
index 273c7c9..020bf3f 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -22,8 +22,8 @@ packages = find:
 python_requires = >= 3.8
 install_requires =
     numpy>=2.0
-    'vam_whittaker@https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp311-cp311-linux_x86_64.whl; python_version=="3.11" and sys_platform=="linux"',
-    'vam_whittaker@https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp312-cp312-linux_x86_64.whl; python_version=="3.12" and sys_platform=="linux"',
+    vam_whittaker @ https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp311-cp311-linux_x86_64.whl;python_version=="3.11"&&sys_platform=="linux"
+    vam_whittaker @ https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp312-cp312-linux_x86_64.whl;python_version=="3.12"&&sys_platform=="linux"
     vam_whittaker; sys_platform=="windows"
     xarray>=0.20.2
     lcmap-pyccd==2021.7.19

From da3d28f0054aa4406771fe3753ee158498439068 Mon Sep 17 00:00:00 2001
From: Jeroen Dries <jeroen.dries@vito.be>
Date: Fri, 8 May 2026 11:56:44 +0200
Subject: [PATCH 18/23] better dep spec

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

diff --git a/setup.cfg b/setup.cfg
index 020bf3f..8c2a741 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -22,8 +22,8 @@ packages = find:
 python_requires = >= 3.8
 install_requires =
     numpy>=2.0
-    vam_whittaker @ https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp311-cp311-linux_x86_64.whl;python_version=="3.11"&&sys_platform=="linux"
-    vam_whittaker @ https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp312-cp312-linux_x86_64.whl;python_version=="3.12"&&sys_platform=="linux"
+    vam_whittaker @ https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp311-cp311-linux_x86_64.whl;python_version=="3.11"
+    vam_whittaker @ https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp312-cp312-linux_x86_64.whl;python_version=="3.12"
     vam_whittaker; sys_platform=="windows"
     xarray>=0.20.2
     lcmap-pyccd==2021.7.19

From 9f5ad9caf25c2b588387951fbbf1cb2508f1b027 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 8 May 2026 10:02:18 +0000
Subject: [PATCH 19/23] ci: use uv for dependency resolution and wheel building

Agent-Logs-Url: https://github.com/Open-EO/FuseTS/sessions/062f5d99-e8b0-4d13-9410-df5583b3e9eb

Co-authored-by: jdries <5937096+jdries@users.noreply.github.com>
---
 .github/workflows/build-wheel.yml   | 12 ++++++------
 .github/workflows/lint-and-test.yml | 10 ++++++----
 2 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/build-wheel.yml b/.github/workflows/build-wheel.yml
index 28b7802..99e1a2d 100644
--- a/.github/workflows/build-wheel.yml
+++ b/.github/workflows/build-wheel.yml
@@ -12,12 +12,12 @@ jobs:
         uses: actions/setup-python@v3
         with:
           python-version: '3.11'
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install wheel
-      - name: Build bdist_wheel
-        run: python setup.py bdist_wheel
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+      - name: Build wheel
+        run: uv build --wheel
       - uses: actions/upload-artifact@v3
         with:
           path: dist/*.whl
\ No newline at end of file
diff --git a/.github/workflows/lint-and-test.yml b/.github/workflows/lint-and-test.yml
index a769d3d..220ce77 100644
--- a/.github/workflows/lint-and-test.yml
+++ b/.github/workflows/lint-and-test.yml
@@ -34,14 +34,16 @@ jobs:
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
       - name: Install dependencies
         run: |
           sudo apt-get update
           sudo apt-get install --yes libopenblas-dev
-          python -m pip install --upgrade pip
-          pip install flake8 pytest
-          pip install cython
-          pip install .[dev] --extra-index-url https://artifactory.vgt.vito.be/artifactory/api/pypi/python-packages-public/simple
+          uv pip install --system flake8 pytest cython
+          uv pip install --system .[dev] --extra-index-url https://artifactory.vgt.vito.be/artifactory/api/pypi/python-packages-public/simple
       - name: Lint with flake8
         run: |
           # stop the build if there are Python syntax errors or undefined names

From cc6058696d9ef5c5727152641443f636df136034 Mon Sep 17 00:00:00 2001
From: Jeroen Dries <jeroen.dries@vito.be>
Date: Fri, 8 May 2026 12:07:14 +0200
Subject: [PATCH 20/23] more spaces again...

---
 setup.cfg | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index 8c2a741..0aef904 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -22,9 +22,9 @@ packages = find:
 python_requires = >= 3.8
 install_requires =
     numpy>=2.0
-    vam_whittaker @ https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp311-cp311-linux_x86_64.whl;python_version=="3.11"
-    vam_whittaker @ https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp312-cp312-linux_x86_64.whl;python_version=="3.12"
-    vam_whittaker; sys_platform=="windows"
+    vam_whittaker @ https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp311-cp311-linux_x86_64.whl ; python_version == "3.11"
+    vam_whittaker @ https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp312-cp312-linux_x86_64.whl ; python_version == "3.12"
+    vam_whittaker ; sys_platform=="windows"
     xarray>=0.20.2
     lcmap-pyccd==2021.7.19
     openeo

From 045abcc7770d77be65df2bb2e3f130811c42efb1 Mon Sep 17 00:00:00 2001
From: Jeroen Dries <jeroen.dries@vito.be>
Date: Fri, 8 May 2026 12:17:03 +0200
Subject: [PATCH 21/23] update index strategy

---
 .github/workflows/lint-and-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/lint-and-test.yml b/.github/workflows/lint-and-test.yml
index 220ce77..65b29da 100644
--- a/.github/workflows/lint-and-test.yml
+++ b/.github/workflows/lint-and-test.yml
@@ -43,7 +43,7 @@ jobs:
           sudo apt-get update
           sudo apt-get install --yes libopenblas-dev
           uv pip install --system flake8 pytest cython
-          uv pip install --system .[dev] --extra-index-url https://artifactory.vgt.vito.be/artifactory/api/pypi/python-packages-public/simple
+          uv pip install --system .[dev] --index-strategy unsafe-best-match --extra-index-url https://artifactory.vgt.vito.be/artifactory/api/pypi/python-packages-public/simple
       - name: Lint with flake8
         run: |
           # stop the build if there are Python syntax errors or undefined names

From e1d9af79d3a506bcbe76217aa9d0e652ab7d4bf9 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 8 May 2026 10:25:37 +0000
Subject: [PATCH 22/23] fix: replace deprecated np.in1d with np.isin for numpy
 2.0

Agent-Logs-Url: https://github.com/Open-EO/FuseTS/sessions/4d248566-b245-4fd8-8c81-91296fb8d73f

Co-authored-by: jdries <5937096+jdries@users.noreply.github.com>
---
 src/fusets/whittaker.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/fusets/whittaker.py b/src/fusets/whittaker.py
index e027324..9aee581 100644
--- a/src/fusets/whittaker.py
+++ b/src/fusets/whittaker.py
@@ -103,7 +103,7 @@ def whittaker(
 
     def callback(timeseries):
         _, _, Zd, XXd = whittaker_f(dates, timeseries, smoothing_lambda, 1)
-        dates_mask = np.in1d(XXd, output_dates)
+        dates_mask = np.isin(XXd, output_dates)
         return Zd[dates_mask]
 
     result = xarray.apply_ufunc(

From 3efbbf26d63fd412a07fa2e9b0317e5516436235 Mon Sep 17 00:00:00 2001
From: Jeroen Dries <jeroen.dries@vito.be>
Date: Fri, 8 May 2026 12:30:30 +0200
Subject: [PATCH 23/23] cleanup

---
 .github/workflows/lint-and-test.yml | 2 --
 setup.cfg                           | 4 ++--
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/lint-and-test.yml b/.github/workflows/lint-and-test.yml
index 65b29da..fadd32a 100644
--- a/.github/workflows/lint-and-test.yml
+++ b/.github/workflows/lint-and-test.yml
@@ -40,8 +40,6 @@ jobs:
           enable-cache: true
       - name: Install dependencies
         run: |
-          sudo apt-get update
-          sudo apt-get install --yes libopenblas-dev
           uv pip install --system flake8 pytest cython
           uv pip install --system .[dev] --index-strategy unsafe-best-match --extra-index-url https://artifactory.vgt.vito.be/artifactory/api/pypi/python-packages-public/simple
       - name: Lint with flake8
diff --git a/setup.cfg b/setup.cfg
index 0aef904..c4c216f 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -22,8 +22,8 @@ packages = find:
 python_requires = >= 3.8
 install_requires =
     numpy>=2.0
-    vam_whittaker @ https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp311-cp311-linux_x86_64.whl ; python_version == "3.11"
-    vam_whittaker @ https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp312-cp312-linux_x86_64.whl ; python_version == "3.12"
+    vam_whittaker @ https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp311-cp311-linux_x86_64.whl ; python_version == "3.11" and sys_platform == "linux"
+    vam_whittaker @ https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp312-cp312-linux_x86_64.whl ; python_version == "3.12" and sys_platform == "linux"
     vam_whittaker ; sys_platform=="windows"
     xarray>=0.20.2
     lcmap-pyccd==2021.7.19