From 5a8b82cb8ac8415278b3b9cef260501f18e4f90b Mon Sep 17 00:00:00 2001 From: Tom Palmer Date: Fri, 5 Dec 2025 13:44:03 +0000 Subject: [PATCH 01/10] Delete accidental whitespace --- pyproject.toml | 1 - 1 file changed, 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 626e370..0d36051 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -44,7 +44,6 @@ dependencies = [ Homepage = "https://github.com/CausalInference/pySEQTarget" Repository = "https://github.com/CausalInference/pySEQTarget" "Bug Tracker" = "https://github.com/CausalInference/pySEQTarget/issues" - "Ryan O'Dea (ORCID)" = "https://orcid.org/0009-0000-0103-9546" "Alejandro Szmulewicz (ORCID)" = "https://orcid.org/0000-0002-2664-802X" "Tom Palmer (ORCID)" = "https://orcid.org/0000-0003-4655-4511" From 2de7f1cb0d0f549f32199774749bb5989179508c Mon Sep 17 00:00:00 2001 From: Tom Palmer Date: Fri, 5 Dec 2025 13:45:58 +0000 Subject: [PATCH 02/10] Add dependency-groups section with pytest --- pyproject.toml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 0d36051..599fb1a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -51,6 +51,11 @@ Repository = "https://github.com/CausalInference/pySEQTarget" "University of Bristol (ROR)" = "https://ror.org/0524sp257" "Harvard University (ROR)" = "https://ror.org/03vek6s52" +[dependency-groups] +dev = [ + "pytest", +] + [tool.setuptools.packages.find] where = ["."] include = ["pySEQTarget*"] From 2471504a53fe4a12e153621b8e8138f8a9acb8af Mon Sep 17 00:00:00 2001 From: Tom Palmer Date: Fri, 5 Dec 2025 13:47:35 +0000 Subject: [PATCH 03/10] Bump checkout to v6 --- .github/workflows/autoformat.yml | 2 +- .github/workflows/publish.yml | 2 +- .github/workflows/python-app.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/autoformat.yml b/.github/workflows/autoformat.yml index 2dcf15c..eb244f6 100644 --- a/.github/workflows/autoformat.yml +++ b/.github/workflows/autoformat.yml @@ -8,7 +8,7 @@ jobs: format: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 with: token: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 1fa8189..e24fd14 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -20,7 +20,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - uses: actions/setup-python@v5 with: diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml index f5c07ac..d1c5689 100644 --- a/.github/workflows/python-app.yml +++ b/.github/workflows/python-app.yml @@ -19,7 +19,7 @@ jobs: python-version: ["3.10", "3.11", "3.12"] steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v5 From 172040cc2e1beba6d63dc5278969aa0328accba5 Mon Sep 17 00:00:00 2001 From: Tom Palmer Date: Fri, 5 Dec 2025 13:47:51 +0000 Subject: [PATCH 04/10] Fix end of file --- .github/workflows/autoformat.yml | 2 +- .github/workflows/publish.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/autoformat.yml b/.github/workflows/autoformat.yml index eb244f6..2987bea 100644 --- a/.github/workflows/autoformat.yml +++ b/.github/workflows/autoformat.yml @@ -31,4 +31,4 @@ jobs: git config --local user.email "github-actions[bot]@users.noreply.github.com" git config --local user.name "github-actions[bot]" git diff --quiet || (git add -A && git commit -m "Auto-format code") - git push \ No newline at end of file + git push diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index e24fd14..fb96eef 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -67,4 +67,4 @@ jobs: - name: Publish release distributions to PyPI uses: pypa/gh-action-pypi-publish@release/v1 with: - packages-dir: dist/ \ No newline at end of file + packages-dir: dist/ From e5d390a43da24486a7623435214a81ff1b77bf69 Mon Sep 17 00:00:00 2001 From: Tom Palmer Date: Fri, 5 Dec 2025 14:03:15 +0000 Subject: [PATCH 05/10] Add pytest.approx() within assert --- tests/test_parallel.py | 27 +++++++++++++++------------ 1 file changed, 15 insertions(+), 12 deletions(-) diff --git a/tests/test_parallel.py b/tests/test_parallel.py index 2ed0351..1033db5 100644 --- a/tests/test_parallel.py +++ b/tests/test_parallel.py @@ -28,15 +28,18 @@ def test_parallel_ITT(): s.bootstrap() s.fit() matrix = s.outcome_model[0]["outcome"].summary2().tables[1]["Coef."].to_list() - assert matrix == [ - -6.828506035553407, - 0.18935003090041902, - 0.12717241010542563, - 0.033715156987629266, - -0.00014691202235029346, - 0.044566165558944326, - 0.0005787770439053261, - 0.0032906669395295026, - -0.01339242049205771, - 0.20072409918428052, - ] + assert matrix == pytest.approx( + [ + -6.828506035553407, + 0.18935003090041902, + 0.12717241010542563, + 0.033715156987629266, + -0.00014691202235029346, + 0.044566165558944326, + 0.0005787770439053261, + 0.0032906669395295026, + -0.01339242049205771, + 0.20072409918428052, + ], + abs=1e-6, + ) From f1897ba23285992eb33fa8b88a4c8804f07208bd Mon Sep 17 00:00:00 2001 From: Tom Palmer Date: Fri, 5 Dec 2025 14:03:34 +0000 Subject: [PATCH 06/10] Add black and isort to dependency-groups --- pyproject.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 599fb1a..3d24231 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -53,6 +53,8 @@ Repository = "https://github.com/CausalInference/pySEQTarget" [dependency-groups] dev = [ + "black", + "isort", "pytest", ] From ff0ff1bc1732dd136e43891049065fb7f2b8aafc Mon Sep 17 00:00:00 2001 From: Tom Palmer Date: Fri, 5 Dec 2025 14:22:03 +0000 Subject: [PATCH 07/10] Add Python 3.13 and 3.14 --- pyproject.toml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 3d24231..652a7a6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,7 +16,9 @@ classifiers = [ "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", - "Programming Language :: Python :: 3.12" + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", ] authors = [ From 5f1c2c9285cc25c20d738a9b339d7e3ab122d6e9 Mon Sep 17 00:00:00 2001 From: Tom Palmer Date: Fri, 5 Dec 2025 14:24:19 +0000 Subject: [PATCH 08/10] Add Python 3.13 and 3.14 to CI tests --- .github/workflows/python-app.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml index d1c5689..adb9362 100644 --- a/.github/workflows/python-app.yml +++ b/.github/workflows/python-app.yml @@ -16,7 +16,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.10", "3.11", "3.12"] + python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] steps: - uses: actions/checkout@v6 From 806144dd4d9031959a516ba95cb9722554187a92 Mon Sep 17 00:00:00 2001 From: Tom Palmer Date: Fri, 5 Dec 2025 15:09:41 +0000 Subject: [PATCH 09/10] Add dev deps for docs site --- pyproject.toml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 652a7a6..43c8341 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,6 +58,11 @@ dev = [ "black", "isort", "pytest", + "myst-parser", + "piccolo_theme", + "sphinx", + "sphinx-copybutton", + "sphinx-autodoc-typehints", ] [tool.setuptools.packages.find] From aa8d38fb5b368d2b589a84f107d601de2c8693f6 Mon Sep 17 00:00:00 2001 From: Tom Palmer Date: Fri, 5 Dec 2025 15:12:52 +0000 Subject: [PATCH 10/10] Ignore uv.lock --- .gitignore | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.gitignore b/.gitignore index c2179a5..4e28064 100644 --- a/.gitignore +++ b/.gitignore @@ -163,3 +163,6 @@ cython_debug/ # specific files .DS_store + +# uv lock file +uv.lock