From 320334be5f199b20ef6a5cb3bd45f80695d19d16 Mon Sep 17 00:00:00 2001 From: RagnarB83 Date: Fri, 4 Oct 2024 12:23:36 +0200 Subject: [PATCH 01/12] Update python-app-conda.yml --- .github/workflows/python-app-conda.yml | 74 ++++++++++++++------------ 1 file changed, 41 insertions(+), 33 deletions(-) diff --git a/.github/workflows/python-app-conda.yml b/.github/workflows/python-app-conda.yml index 66baefc36..49bde5ba1 100644 --- a/.github/workflows/python-app-conda.yml +++ b/.github/workflows/python-app-conda.yml @@ -14,37 +14,45 @@ jobs: runs-on: ubuntu-latest strategy: max-parallel: 5 - steps: - - uses: actions/checkout@v3 - - name: Set up Python 3.11 - uses: actions/setup-python@v3 - with: - python-version: '3.11' - - name: Add conda to system path - run: | - # $CONDA is an environment variable pointing to the root of the miniconda directory - echo $CONDA/bin >> $GITHUB_PATH - conda --version - - name: Change conda version - run: | - # RB: Bug in the most recent version (24.1.2) - conda install conda=23.11.0 python=3.11 - conda --version - - name: Install dependencies - run: | - conda env update --file environment.yml --name base - - name: Check conda env - run: | - conda list - - name: Lint with flake8 - run: | - conda install flake8 - # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - - name: Test with pytest - run: | - conda install pytest - pytest + - uses: actions/checkout@v4 + - uses: conda-incubator/setup-miniconda@v3 + with: + miniforge-version: latest + python-version: 3.11 + - name: Add conda to system path + run: | + # $CONDA is an environment variable pointing to the root of the miniconda directory + echo $CONDA/bin >> $GITHUB_PATH + conda --version + - run: | + conda info + conda list + conda config --show-sources + conda config --show + printenv | sort + - name: Install dependencies + run: | + conda env update --file environment.yml --name base + - name: Check conda env + run: | + conda list + - name: check stuff + run: | + which python + which conda + which mamba + which pip + echo $PATH + which xtb + - name: Lint with flake8 + run: | + conda install flake8 + # stop the build if there are Python syntax errors or undefined names + flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide + flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + - name: Test with pytest + run: | + conda install pytest + pytest From 744fe037e62557c1a2cc16ae324b3e835bffa2e2 Mon Sep 17 00:00:00 2001 From: RagnarB83 Date: Fri, 4 Oct 2024 12:34:33 +0200 Subject: [PATCH 02/12] Update python-app-conda.yml --- .github/workflows/python-app-conda.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/python-app-conda.yml b/.github/workflows/python-app-conda.yml index 49bde5ba1..9793cb919 100644 --- a/.github/workflows/python-app-conda.yml +++ b/.github/workflows/python-app-conda.yml @@ -55,4 +55,7 @@ jobs: - name: Test with pytest run: | conda install pytest - pytest + which python + pwd + ls + pytest -v From 8685ca24bf33adba330e33d5de076a58ad33c1f3 Mon Sep 17 00:00:00 2001 From: RagnarB83 Date: Fri, 4 Oct 2024 12:42:42 +0200 Subject: [PATCH 03/12] Update python-app-conda.yml --- .github/workflows/python-app-conda.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/python-app-conda.yml b/.github/workflows/python-app-conda.yml index 9793cb919..6fb40e6bc 100644 --- a/.github/workflows/python-app-conda.yml +++ b/.github/workflows/python-app-conda.yml @@ -23,7 +23,8 @@ jobs: - name: Add conda to system path run: | # $CONDA is an environment variable pointing to the root of the miniconda directory - echo $CONDA/bin >> $GITHUB_PATH + #echo $CONDA/bin >> $GITHUB_PATH + conda activate test conda --version - run: | conda info From 3275ec1ee15fd92e23ffcd854124b0b046eb5bea Mon Sep 17 00:00:00 2001 From: RagnarB83 Date: Fri, 4 Oct 2024 12:43:56 +0200 Subject: [PATCH 04/12] Update python-app-conda.yml --- .github/workflows/python-app-conda.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/python-app-conda.yml b/.github/workflows/python-app-conda.yml index 6fb40e6bc..d04d5a249 100644 --- a/.github/workflows/python-app-conda.yml +++ b/.github/workflows/python-app-conda.yml @@ -24,6 +24,7 @@ jobs: run: | # $CONDA is an environment variable pointing to the root of the miniconda directory #echo $CONDA/bin >> $GITHUB_PATH + conda init conda activate test conda --version - run: | From 52a462a3fd0e554977b2460eb13c1fc58fb4c6a6 Mon Sep 17 00:00:00 2001 From: RagnarB83 Date: Fri, 4 Oct 2024 12:44:49 +0200 Subject: [PATCH 05/12] Update python-app-conda.yml --- .github/workflows/python-app-conda.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-app-conda.yml b/.github/workflows/python-app-conda.yml index d04d5a249..7a238aeb0 100644 --- a/.github/workflows/python-app-conda.yml +++ b/.github/workflows/python-app-conda.yml @@ -25,7 +25,7 @@ jobs: # $CONDA is an environment variable pointing to the root of the miniconda directory #echo $CONDA/bin >> $GITHUB_PATH conda init - conda activate test + conda activate test conda --version - run: | conda info From 1fa99b25e057998311dd5d36581bc2e61fe3daea Mon Sep 17 00:00:00 2001 From: RagnarB83 Date: Fri, 4 Oct 2024 12:46:46 +0200 Subject: [PATCH 06/12] Update python-app-conda.yml --- .github/workflows/python-app-conda.yml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/.github/workflows/python-app-conda.yml b/.github/workflows/python-app-conda.yml index 7a238aeb0..8d482b1ae 100644 --- a/.github/workflows/python-app-conda.yml +++ b/.github/workflows/python-app-conda.yml @@ -19,13 +19,10 @@ jobs: - uses: conda-incubator/setup-miniconda@v3 with: miniforge-version: latest - python-version: 3.11 - name: Add conda to system path run: | # $CONDA is an environment variable pointing to the root of the miniconda directory - #echo $CONDA/bin >> $GITHUB_PATH - conda init - conda activate test + echo $CONDA/bin >> $GITHUB_PATH conda --version - run: | conda info From 69f4fe2ad4345a7502358cef7370385696441c5a Mon Sep 17 00:00:00 2001 From: RagnarB83 Date: Fri, 4 Oct 2024 12:55:41 +0200 Subject: [PATCH 07/12] Update environment.yml --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 1d1564462..bb636ad5c 100644 --- a/environment.yml +++ b/environment.yml @@ -4,7 +4,7 @@ channels: - conda-forge #Some basic easy-to-install packages for ASH dependencies: - - python=3.10 + - python=3.11 - pip - openmm - pdbfixer From ae3c4fa57b76c039cdf4d6d9b2a10427cfad614a Mon Sep 17 00:00:00 2001 From: RagnarB83 Date: Fri, 4 Oct 2024 13:00:33 +0200 Subject: [PATCH 08/12] Update python-app-conda.yml --- .github/workflows/python-app-conda.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/python-app-conda.yml b/.github/workflows/python-app-conda.yml index 8d482b1ae..7ea232c3b 100644 --- a/.github/workflows/python-app-conda.yml +++ b/.github/workflows/python-app-conda.yml @@ -15,7 +15,11 @@ jobs: strategy: max-parallel: 5 steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v3 + - name: Set up Python 3.11 + uses: actions/setup-python@v3 + with: + python-version: '3.11' - uses: conda-incubator/setup-miniconda@v3 with: miniforge-version: latest From 4384e2a720a8fba66521495148ca173de59c31b7 Mon Sep 17 00:00:00 2001 From: RagnarB83 Date: Fri, 4 Oct 2024 13:28:35 +0200 Subject: [PATCH 09/12] Update python-app-conda.yml --- .github/workflows/python-app-conda.yml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/.github/workflows/python-app-conda.yml b/.github/workflows/python-app-conda.yml index 7ea232c3b..65bdeb7e7 100644 --- a/.github/workflows/python-app-conda.yml +++ b/.github/workflows/python-app-conda.yml @@ -28,17 +28,12 @@ jobs: # $CONDA is an environment variable pointing to the root of the miniconda directory echo $CONDA/bin >> $GITHUB_PATH conda --version - - run: | conda info conda list conda config --show-sources conda config --show printenv | sort - - name: Install dependencies - run: | conda env update --file environment.yml --name base - - name: Check conda env - run: | conda list - name: check stuff run: | From f0171a32605b0a20317491d41c03741ab44ac34d Mon Sep 17 00:00:00 2001 From: RagnarB83 Date: Fri, 4 Oct 2024 13:44:03 +0200 Subject: [PATCH 10/12] Update python-app-conda.yml --- .github/workflows/python-app-conda.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/python-app-conda.yml b/.github/workflows/python-app-conda.yml index 65bdeb7e7..b1a683b23 100644 --- a/.github/workflows/python-app-conda.yml +++ b/.github/workflows/python-app-conda.yml @@ -52,6 +52,7 @@ jobs: flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - name: Test with pytest run: | + export PYTHONPATH=/home/runner/work/ash/ash:$PYTHONPATH conda install pytest which python pwd From e41b2e0057e278a0e7cab53b23198968c4ace76c Mon Sep 17 00:00:00 2001 From: RagnarB83 Date: Fri, 4 Oct 2024 13:49:42 +0200 Subject: [PATCH 11/12] Update python-app-conda.yml --- .github/workflows/python-app-conda.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/python-app-conda.yml b/.github/workflows/python-app-conda.yml index b1a683b23..1170690f2 100644 --- a/.github/workflows/python-app-conda.yml +++ b/.github/workflows/python-app-conda.yml @@ -50,9 +50,11 @@ jobs: flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + - name: set pythonpath + run: | + echo "export PYTHONPATH=/home/runner/work/ash/ash:$PYTHONPATH" >> $GITHUB_ENV - name: Test with pytest run: | - export PYTHONPATH=/home/runner/work/ash/ash:$PYTHONPATH conda install pytest which python pwd From eb5753a35287ad05a4928bc1b86e4257eed2e4f4 Mon Sep 17 00:00:00 2001 From: RagnarB83 Date: Fri, 4 Oct 2024 13:55:58 +0200 Subject: [PATCH 12/12] Update python-app-conda.yml --- .github/workflows/python-app-conda.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/python-app-conda.yml b/.github/workflows/python-app-conda.yml index 1170690f2..a947a0aab 100644 --- a/.github/workflows/python-app-conda.yml +++ b/.github/workflows/python-app-conda.yml @@ -50,13 +50,11 @@ jobs: flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - - name: set pythonpath - run: | - echo "export PYTHONPATH=/home/runner/work/ash/ash:$PYTHONPATH" >> $GITHUB_ENV - name: Test with pytest run: | conda install pytest which python pwd ls + export PYTHONPATH=/home/runner/work/ash/ash:$PYTHONPATH pytest -v