From f980d8614d82a688b36f3867a4e5751b875a53c2 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Wed, 18 Oct 2023 17:06:09 +0200 Subject: [PATCH 01/12] GHA: test python3.12 --- .github/workflows/test_python_ver_matrix.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_python_ver_matrix.yml b/.github/workflows/test_python_ver_matrix.yml index 59dcf91041..84cd8a484f 100644 --- a/.github/workflows/test_python_ver_matrix.yml +++ b/.github/workflows/test_python_ver_matrix.yml @@ -25,7 +25,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.9', '3.10', '3.11'] + python-version: ['3.9', '3.10', '3.11', '3.12'] experimental: [false] steps: From 993e617b5da3015df2ffba35854293acde2b730f Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Wed, 18 Oct 2023 19:31:55 +0200 Subject: [PATCH 02/12] Why setuptools<64? Remove. --- scripts/installAmiciSource.sh | 1 - 1 file changed, 1 deletion(-) diff --git a/scripts/installAmiciSource.sh b/scripts/installAmiciSource.sh index aa330bef22..93482be291 100755 --- a/scripts/installAmiciSource.sh +++ b/scripts/installAmiciSource.sh @@ -27,7 +27,6 @@ else source ${AMICI_PATH}/build/venv/bin/activate fi -pip install -U "setuptools<64" pip install --upgrade pip wheel pip install --upgrade pip scipy matplotlib coverage pytest \ pytest-cov cmake_build_extension numpy From 90e5da4ffcf793a6b2ea532eae5e648d74f31826 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Mon, 23 Oct 2023 07:57:42 +0200 Subject: [PATCH 03/12] dateutil --- .github/workflows/test_python_ver_matrix.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/test_python_ver_matrix.yml b/.github/workflows/test_python_ver_matrix.yml index 84cd8a484f..26e7ab43b9 100644 --- a/.github/workflows/test_python_ver_matrix.yml +++ b/.github/workflows/test_python_ver_matrix.yml @@ -55,6 +55,10 @@ jobs: - name: Build BNGL run: | scripts/buildBNGL.sh + + # until https://github.com/dateutil/dateutil >2.8.2 is released + - run: pip install https://github.com/dateutil/dateutil/archive/296d419fe6bf3b22897f8f210735ac9c4e1cb796.zip + - name: Install python package run: | scripts/installAmiciSource.sh From f77f6cfc6abd3f545581ca994d31e01576650cb1 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Mon, 23 Oct 2023 08:04:41 +0200 Subject: [PATCH 04/12] .. --- .github/workflows/test_python_ver_matrix.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_python_ver_matrix.yml b/.github/workflows/test_python_ver_matrix.yml index 26e7ab43b9..ab8a4e3e2f 100644 --- a/.github/workflows/test_python_ver_matrix.yml +++ b/.github/workflows/test_python_ver_matrix.yml @@ -57,7 +57,7 @@ jobs: scripts/buildBNGL.sh # until https://github.com/dateutil/dateutil >2.8.2 is released - - run: pip install https://github.com/dateutil/dateutil/archive/296d419fe6bf3b22897f8f210735ac9c4e1cb796.zip + - run: pip install git+https://github.com/dateutil/dateutil.git@296d419fe6bf3b22897f8f210735ac9c4e1cb796 - name: Install python package run: | From 8abc37de303649968751511b2f8f71079b1e4aaf Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Mon, 23 Oct 2023 08:40:36 +0200 Subject: [PATCH 05/12] .. --- .github/workflows/test_python_ver_matrix.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/test_python_ver_matrix.yml b/.github/workflows/test_python_ver_matrix.yml index ab8a4e3e2f..2ffc691668 100644 --- a/.github/workflows/test_python_ver_matrix.yml +++ b/.github/workflows/test_python_ver_matrix.yml @@ -56,13 +56,13 @@ jobs: run: | scripts/buildBNGL.sh - # until https://github.com/dateutil/dateutil >2.8.2 is released - - run: pip install git+https://github.com/dateutil/dateutil.git@296d419fe6bf3b22897f8f210735ac9c4e1cb796 - - name: Install python package run: | scripts/installAmiciSource.sh + # until https://github.com/dateutil/dateutil >2.8.2 is released + - run: source build/venv/bin/activate && pip3 install git+https://github.com/dateutil/dateutil.git@296d419fe6bf3b22897f8f210735ac9c4e1cb796 + - name: Python tests run: | source build/venv/bin/activate \ From 50e527ce95c2c0f2bdd562be5073dbde920dc62d Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Fri, 3 Nov 2023 05:48:50 +0100 Subject: [PATCH 06/12] .. --- .github/workflows/test_python_ver_matrix.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_python_ver_matrix.yml b/.github/workflows/test_python_ver_matrix.yml index 2ffc691668..a0f3072ec9 100644 --- a/.github/workflows/test_python_ver_matrix.yml +++ b/.github/workflows/test_python_ver_matrix.yml @@ -60,7 +60,7 @@ jobs: run: | scripts/installAmiciSource.sh - # until https://github.com/dateutil/dateutil >2.8.2 is released + # until https://github.com/dateutil/dateutil >2.8.2 is released https://github.com/dateutil/dateutil/issues/1314 - run: source build/venv/bin/activate && pip3 install git+https://github.com/dateutil/dateutil.git@296d419fe6bf3b22897f8f210735ac9c4e1cb796 - name: Python tests From 4e6e5c4c4f2ab22ebd1754ac441fc93dc7d1783c Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Thu, 16 Nov 2023 11:19:14 +0100 Subject: [PATCH 07/12] test_pypi.yml --- .github/workflows/test_pypi.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_pypi.yml b/.github/workflows/test_pypi.yml index f8150aa42e..68675c578a 100644 --- a/.github/workflows/test_pypi.yml +++ b/.github/workflows/test_pypi.yml @@ -11,7 +11,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: [3.9, 3.9, '3.10'] + python-version: ["3.9", "3.10", "3.11", "3.12"] os: [ubuntu-22.04, macos-latest] runs-on: ${{ matrix.os }} From 3f65f048faa87e21dafd3a40a880c8630f9c58c1 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Thu, 14 Dec 2023 21:07:16 +0100 Subject: [PATCH 08/12] sympy-master --- .github/workflows/test_python_ver_matrix.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/test_python_ver_matrix.yml b/.github/workflows/test_python_ver_matrix.yml index 9b2b1a850a..a928bdffb7 100644 --- a/.github/workflows/test_python_ver_matrix.yml +++ b/.github/workflows/test_python_ver_matrix.yml @@ -52,6 +52,11 @@ jobs: # until https://github.com/dateutil/dateutil >2.8.2 is released https://github.com/dateutil/dateutil/issues/1314 - run: source build/venv/bin/activate && pip3 install git+https://github.com/dateutil/dateutil.git@296d419fe6bf3b22897f8f210735ac9c4e1cb796 + if: matrix.python-version == '3.12' + + # until sympy>1.12 is released + - run: source build/venv/bin/activate && pip3 install git+https://github.com/sympy/sympy.git@master + if: matrix.python-version == '3.12' - name: Python tests run: | From f3d6efede6aecb92dd5dd508b73acdd4eeb332d1 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Thu, 14 Dec 2023 21:53:06 +0100 Subject: [PATCH 09/12] .. --- .github/workflows/test_python_ver_matrix.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_python_ver_matrix.yml b/.github/workflows/test_python_ver_matrix.yml index a928bdffb7..36f73a68c0 100644 --- a/.github/workflows/test_python_ver_matrix.yml +++ b/.github/workflows/test_python_ver_matrix.yml @@ -55,7 +55,7 @@ jobs: if: matrix.python-version == '3.12' # until sympy>1.12 is released - - run: source build/venv/bin/activate && pip3 install git+https://github.com/sympy/sympy.git@master + - run: pip3 install git+https://github.com/sympy/sympy.git@master if: matrix.python-version == '3.12' - name: Python tests From 73373646742b06b21d1808a24fbddf1828cf992b Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Thu, 14 Dec 2023 22:38:50 +0100 Subject: [PATCH 10/12] Revert ".." This reverts commit f3d6efede6aecb92dd5dd508b73acdd4eeb332d1. --- .github/workflows/test_python_ver_matrix.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_python_ver_matrix.yml b/.github/workflows/test_python_ver_matrix.yml index 36f73a68c0..a928bdffb7 100644 --- a/.github/workflows/test_python_ver_matrix.yml +++ b/.github/workflows/test_python_ver_matrix.yml @@ -55,7 +55,7 @@ jobs: if: matrix.python-version == '3.12' # until sympy>1.12 is released - - run: pip3 install git+https://github.com/sympy/sympy.git@master + - run: source build/venv/bin/activate && pip3 install git+https://github.com/sympy/sympy.git@master if: matrix.python-version == '3.12' - name: Python tests From 299f47a390eb85e0e61e05fd03e1389ac7b0bbec Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Thu, 14 Dec 2023 22:41:47 +0100 Subject: [PATCH 11/12] .. --- .github/workflows/test_python_ver_matrix.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test_python_ver_matrix.yml b/.github/workflows/test_python_ver_matrix.yml index a928bdffb7..b78abfcb8c 100644 --- a/.github/workflows/test_python_ver_matrix.yml +++ b/.github/workflows/test_python_ver_matrix.yml @@ -54,6 +54,9 @@ jobs: - run: source build/venv/bin/activate && pip3 install git+https://github.com/dateutil/dateutil.git@296d419fe6bf3b22897f8f210735ac9c4e1cb796 if: matrix.python-version == '3.12' + # install pysb before sympy to allow for sympy>=1.12 (https://github.com/pysb/pysb/commit/e83937cb8c74afc9b2fa96595b68464946745f33) + - run: source build/venv/bin/activate && pip3 install git+https://github.com/pysb/pysb + # until sympy>1.12 is released - run: source build/venv/bin/activate && pip3 install git+https://github.com/sympy/sympy.git@master if: matrix.python-version == '3.12' @@ -61,6 +64,5 @@ jobs: - name: Python tests run: | source build/venv/bin/activate \ - && pip3 install git+https://github.com/pysb/pysb \ && python3 -m pytest --ignore-glob=*petab* \ --ignore-glob=*test_splines.py ${AMICI_DIR}/python/tests From 00aae73d725eae5cc79ff279ff422f6783f6cbdf Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Thu, 14 Dec 2023 23:07:32 +0100 Subject: [PATCH 12/12] .. --- .github/workflows/test_python_ver_matrix.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test_python_ver_matrix.yml b/.github/workflows/test_python_ver_matrix.yml index b78abfcb8c..9290cd0c1a 100644 --- a/.github/workflows/test_python_ver_matrix.yml +++ b/.github/workflows/test_python_ver_matrix.yml @@ -64,5 +64,7 @@ jobs: - name: Python tests run: | source build/venv/bin/activate \ - && python3 -m pytest --ignore-glob=*petab* \ + && python3 -m pytest \ + --durations=10 \ + --ignore-glob=*petab* \ --ignore-glob=*test_splines.py ${AMICI_DIR}/python/tests