Splits tests according to their environments in CI

.github/workflows/python-tox-testing-including-conda.yml → .github/workflows/python-tox-testing-base.yml

@@ -1,4 +1,4 @@
-name: Tests on poli (dev, conda, python 3.9)
+name: poli base (dev, conda, python 3.9)
 
 on: [push]
 
@@ -24,6 +24,6 @@ jobs:
     - name: Test linting with tox
       run: |
         tox -c tox.ini -e lint
-    - name: Test poli-base with tox (ignoring RaSP)
+    - name: Test basic behaviors of poli with tox and pytest
       run: |
-        tox -c tox.ini -e poli-base-py39 -- --ignore=src/poli/tests/registry/proteins/test_rasp.py
+        tox -c tox.ini -e poli-base-py39

.github/workflows/python-tox-testing-dockstring-env.yml

@@ -0,0 +1,26 @@
+name: poli dockstring (dev, conda, python 3.9)
+
+on: [push]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.9'
+    - 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
+    - name: Install dependencies
+      run: |
+        python -m pip install tox
+    - name: Test dockstring-related black boxes with tox and pytest
+      run: |
+        tox -c tox.ini -e poli-dockstring-py39

.github/workflows/python-tox-testing-lambo-env.yml

@@ -0,0 +1,26 @@
+name: poli lambo (dev, conda, python 3.9)
+
+on: [push]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.9'
+    - 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
+    - name: Install dependencies
+      run: |
+        python -m pip install tox
+    - name: Test lambo-related black boxes with tox and pytest
+      run: |
+        tox -c tox.ini -e poli-lambo-py39

.github/workflows/python-tox-testing-protein-env.yml

@@ -0,0 +1,26 @@
+name: poli protein (dev, conda, python 3.9)
+
+on: [push]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.9'
+    - 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
+    - name: Install dependencies
+      run: |
+        python -m pip install tox
+    - name: Test protein-related black boxes with tox and pytest
+      run: |
+        tox -c tox.ini -e poli-protein-py39

.github/workflows/python-tox-testing-tdc-env.yml

@@ -0,0 +1,26 @@
+name: poli tdc (dev, conda, python 3.9)
+
+on: [push]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.9'
+    - 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
+    - name: Install dependencies
+      run: |
+        python -m pip install tox
+    - name: Test PyTDC-related black boxes with tox and pytest
+      run: |
+        tox -c tox.ini -e poli-tdc-py39

pyproject.toml

@@ -42,5 +42,5 @@ markers = [
     "poli__tdc: marks tests that run in the poli__tdc environment",
     "poli__protein: marks tests that run in the poli__protein environment",
     "poli__rasp: marks tests that run in the poli__rasp environment",
-    "unmarked: All unmarked tests",
+    "unmarked: All other tests, which usually run in the base environment",
 ]

tox.ini

@@ -2,6 +2,10 @@
 env_list =
     lint
     poli-base-py39
+    poli-dockstring-py39
+    poli-tdc-py39
+    poli-protein-py39
+    poli-rasp-py39
 minversion = 4.10.0
 
 [testenv]
@@ -15,27 +19,6 @@ deps =
 commands =
     sh -c "rm -rf ~/.poli_objectives/*.sh"
     sh -c "rm -rf ~/.poli_objectives/config.rc"
-    sh -c 'if conda info --envs | grep -q poli__base; then echo "poli__base already exists"; else conda env create -f ./src/poli/objective_repository/aloha/environment.yml; fi'
-    sh -c "conda run -n poli__base python -m pip uninstall -y poli"
-    sh -c "conda run -n poli__base python -m pip install -e ."
-    sh -c 'if conda info --envs | grep -q poli__chem; then echo "poli__chem already exists"; else conda env create -f ./src/poli/objective_repository/rdkit_qed/environment.yml; fi'
-    sh -c "conda run -n poli__chem python -m pip uninstall -y poli"
-    sh -c "conda run -n poli__chem python -m pip install -e ."
-    sh -c 'if conda info --envs | grep -q poli__protein; then echo "poli__protein already exists"; else conda env create -f ./src/poli/objective_repository/foldx_stability/environment.yml; fi'
-    sh -c "conda run -n poli__protein python -m pip uninstall -y poli"
-    sh -c "conda run -n poli__protein python -m pip install -e ."
-    sh -c 'if conda info --envs | grep -q poli__dockstring; then echo "poli__dockstring already exists"; else conda env create -f ./src/poli/objective_repository/dockstring/environment.yml; fi'
-    sh -c "conda run -n poli__dockstring python -m pip uninstall -y poli"
-    sh -c "conda run -n poli__dockstring python -m pip install -e ."
-    sh -c 'if conda info --envs | grep -q poli__tdc; then echo "poli__tdc already exists"; else conda env create -f ./src/poli/core/chemistry/environment.yml; fi'
-    sh -c "conda run -n poli__tdc python -m pip uninstall -y poli"
-    sh -c "conda run -n poli__tdc python -m pip install -e ."
-    sh -c 'if conda info --envs | grep -q poli__lambo; then echo "poli__lambo already exists"; else conda env create -f ./src/poli/objective_repository/foldx_rfp_lambo/environment.yml; fi'
-    sh -c "conda run -n poli__lambo python -m pip uninstall -y poli"
-    sh -c "conda run -n poli__lambo python -m pip install -e ."
-    pytest {tty:--color=yes} -v -m "not slow" {posargs}
-    sh -c "rm -rf ~/.poli_objectives/*.sh"
-    sh -c "rm -rf ~/.poli_objectives/config.rc"
 
 [testenv:lint]
 description = check the code style with black
@@ -54,3 +37,75 @@ deps=
     -e.
 commands=
     {[testenv]commands}
+    pytest {tty:--color=yes} -v -m "unmarked" {posargs}
+
+[testenv:poli-tdc-py39]
+description = run the tests with pytest on the TDC environment for poli
+basepython = python3.9
+wheel_build_env = .pkg
+deps=
+    {[testenv]deps}
+    -r requirements.txt
+    -e.
+commands=
+    sh -c 'if conda info --envs | grep -q poli__tdc; then echo "poli__tdc already exists"; else conda env create -f ./src/poli/core/chemistry/environment.yml; fi'
+    sh -c "conda run -n poli__tdc python -m pip uninstall -y poli"
+    sh -c "conda run -n poli__tdc python -m pip install -e ."
+    pytest {tty:--color=yes} -v -m "not slow and poli__tdc" {posargs}
+
+[testenv:poli-protein-py39]
+description = run the tests with pytest on the protein environment for poli
+basepython = python3.9
+wheel_build_env = .pkg
+deps=
+    {[testenv]deps}
+    -r requirements.txt
+    -e.
+commands=
+    sh -c 'if conda info --envs | grep -q poli__protein; then echo "poli__protein already exists"; else conda env create -f ./src/poli/objective_repository/foldx_stability/environment.yml; fi'
+    sh -c "conda run -n poli__protein python -m pip uninstall -y poli"
+    sh -c "conda run -n poli__protein python -m pip install -e ."
+    pytest {tty:--color=yes} -v -m "not slow and poli__protein" {posargs}
+
+[testenv:poli-lambo-py39]
+description = run the tests with pytest on the lambo environment for poli
+basepython = python3.9
+wheel_build_env = .pkg
+deps=
+    {[testenv]deps}
+    -r requirements.txt
+    -e.
+commands=
+    sh -c 'if conda info --envs | grep -q poli__lambo; then echo "poli__lambo already exists"; else conda env create -f ./src/poli/objective_repository/foldx_rfp_lambo/environment.yml; fi'
+    sh -c "conda run -n poli__lambo python -m pip uninstall -y poli"
+    sh -c "conda run -n poli__lambo python -m pip install -e ."
+    pytest {tty:--color=yes} -v -m "not slow and poli__lambo" {posargs}
+
+[testenv:poli-dockstring-py39]
+description = run the tests with pytest on the dockstring environment for poli
+basepython = python3.9
+wheel_build_env = .pkg
+deps=
+    {[testenv]deps}
+    -r requirements.txt
+    -e.
+commands=
+    sh -c 'if conda info --envs | grep -q poli__dockstring; then echo "poli__dockstring already exists"; else conda env create -f ./src/poli/objective_repository/dockstring/environment.yml; fi'
+    sh -c "conda run -n poli__dockstring python -m pip uninstall -y poli"
+    sh -c "conda run -n poli__dockstring python -m pip install -e ."
+    pytest {tty:--color=yes} -v -m "not slow and poli__dockstring" {posargs}
+
+[testenv:poli-rasp-py39]
+description = run the tests with pytest on the dockstring environment for poli
+basepython = python3.9
+wheel_build_env = .pkg
+deps=
+    {[testenv]deps}
+    -r requirements.txt
+    -e.
+commands=
+    sh -c 'if conda info --envs | grep -q poli__rasp; then echo "poli__rasp already exists"; else conda env create -f ./src/poli/objective_repository/rasp/environment.yml; fi'
+    sh -c "conda run -n poli__rasp python -m pip uninstall -y poli"
+    sh -c "conda run -n poli__rasp python -m pip install -e ."
+    pytest {tty:--color=yes} -v -m "not slow and poli__rasp" {posargs}
+