test: run test with gh actions in docker

.github/workflows/ci.yml

@@ -9,7 +9,7 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: psf/black@stable
   release:
     name: release
@@ -23,7 +23,7 @@ jobs:
         with:
           release-type: python
           package-name: kimmdy
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: tag stable versions
         if: ${{ steps.release.outputs.release_created }}
         run: |
@@ -34,3 +34,35 @@ jobs:
           git push origin :stable || true
           git tag -a stable -m "Last Stable Release"
           git push origin stable
+  prlabel:
+    runs-on: ubuntu-latest
+    outputs:
+      status: ${{ steps.prcheck.conclusion }}
+    steps:
+      - name: Check pr lable
+        id: prcheck
+        uses: jesusvasquez333/verify-pr-label-action@v1.4.0
+        with:
+          github-token: '${{ secrets.GITHUB_TOKEN }}'
+          valid-labels: 'CI:run_test'
+          invalid-labels: ''
+          disable-reviews: true
+  test:
+    runs-on: ubuntu-latest
+    container: riedmiki/gromacs-plumed-python:2021
+    needs: prlabel
+    if: needs.prlabel.outputs.status == 'success'
+    steps:
+      - uses  : actions/checkout@v3
+      - name: run tox
+        run: tox
+      - name: zip coverage report
+        if: ${{ !cancelled() }}
+        run: zip -r htmlcov.zip htmlcov || true
+      - uses: actions/upload-artifact@v3
+        if: ${{ !cancelled() }}
+        with:
+          name: coverage artifact
+          path: htmlcov.zip
+
+

.gitignore

@@ -68,7 +68,9 @@ pip-log.txt
 pip-delete-this-directory.txt
 
 # Unit test / coverage reports
+artifacts
 htmlcov/
+htmlcov*
 .tox/
 .nox/
 .coverage

README.md

@@ -1,5 +1,7 @@
 # KIMMDY
 
+[![CI](https://github.com/hits-mbm-dev/kimmdy/actions/workflows/ci.yml/badge.svg)](https://github.com/hits-mbm-dev/kimmdy/actions/workflows/ci.yml)
+
 Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics (KIMMDY)
 
 ## Quick start
@@ -8,8 +10,16 @@ Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics
 * `cd kimmdy`
 * `python -m venv .venv`
 * `source ./venv/bin/activate`
+* `python -m pip install -e ./`
+* Some rections need a GROMACS version patched with PLUMED, gromacs name should then contain `MODIFIED` or `plumed`
+
+## Development setup
+
 * `python -m pip install -r requirments.txt`
-* Some rections need a GROMACS version patched with PLUMED
+* code style: black
+* docstrings: numpy
+* [Conventional commit](https://www.conventionalcommits.org/en/v1.0.0/) messages when possible for pretty release notes.
+
 
 ## First simulation
 
@@ -19,3 +29,14 @@ Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics
 * check output: `kimmdy.log`, `test_out_00X/`
 
 
+## Local testing
+
+For developoment, we provide a docker image containing gromacs and multiple python versions to test against.  
+To run the test locally, you must:
+- install docker
+- install [act](https://github.com/nektos/act), easiest option is with github cli
+    - install github cli (`gh`)
+    - `gh extension install https://github.com/nektos/gh-act`
+- run tests with `gh extension exec act -j test --artifact-server-path ./artifacts`
+    - customize which python versions to test in `tox.ini` 
+    - html coverage report is exported into `artifacts`

plugins/setup.cfg

@@ -17,7 +17,6 @@ package_dir =
     =src
 include_package_data = True
 install_requires =
-    kimmdy
     MDAnalysis
 
 python_requires = >= 3.9

requirements.txt

@@ -3,7 +3,7 @@ tox
 black
 hypothesis
 jupyter
-git+https://github.com/machow/quartodoc.git
+# git+https://github.com/machow/quartodoc.git   
 pydantic<2
 -e .
 -e ./plugins

src/kimmdy/utils.py

@@ -169,7 +169,7 @@ def check_gmx_version(config):
     """Check for an existing gromacs installation.
 
     If PLUMED is meant to be used it additionally checks for the keyword
-    'MODIFIED' in the version name.
+    'MODIFIED' or 'plumed' in the version name.
     """
     try:
         version = [
@@ -184,18 +184,13 @@ def check_gmx_version(config):
         logging.error(m)
         raise SystemError(m)
 
-    # this should probably be a TODO: then
-    # i hate this
-    if (
-        any(
-            "plumed" in y
-            for y in [
-                config.mds.attr(x).get_attributes() for x in config.mds.get_attributes()
-            ]
-        )
-        and not "MODIFIED" in version
-    ):
-        m = "GROMACS version does not contain MODIFIED, aborting due to lack of PLUMED patch."
+    if any(
+        "plumed" in y
+        for y in [
+            config.mds.attr(x).get_attributes() for x in config.mds.get_attributes()
+        ]
+    ) and (not ("MODIFIED" in version or "plumed" in version)):
+        m = "GROMACS version does not contain MODIFIED or plumed, aborting due to lack of PLUMED patch."
         logging.error(m)
         logging.error("Version was: " + version)
         if not config.dryrun:

tests/test_integration.py

@@ -78,6 +78,7 @@ def test_grompp_with_kimmdy_topology(tmp_path):
     )
 
 
+@pytest.mark.slow
 def test_integration_hat_reaction(tmp_path, caplog):
     testdir = setup_testdir(tmp_path, "hat_naive")
     caplog.set_level(logging.INFO)
@@ -91,6 +92,7 @@ def test_integration_hat_reaction(tmp_path, caplog):
     )
 
 
+@pytest.mark.slow
 def test_integration_homolysis_reaction(tmp_path, caplog):
     testdir = setup_testdir(tmp_path, "homolysis")
     caplog.set_level(logging.INFO)
@@ -105,6 +107,7 @@ def test_integration_homolysis_reaction(tmp_path, caplog):
     )
 
 
+@pytest.mark.slow
 def test_integration_whole_run(tmp_path, caplog):
     testdir = setup_testdir(tmp_path, "whole_run")
     caplog.set_level(logging.INFO)

tests/test_topology.py

@@ -244,7 +244,10 @@ def test_break_bind_bond_hexala(self, hexala_top_fix):
         assert top.improper_dihedrals == og_top.improper_dihedrals
 
     @given(bondindex=st.integers(min_value=0, max_value=70))
-    @settings(suppress_health_check=[HealthCheck.function_scoped_fixture])
+    @settings(
+        suppress_health_check=[HealthCheck.function_scoped_fixture], deadline=1000
+    )
+    @pytest.mark.slow
     def test_break_bind_random_bond_hexala(self, hexala_top_fix, bondindex):
         top = deepcopy(hexala_top_fix)
         og_top = deepcopy(top)

tox.ini

@@ -1,13 +1,50 @@
 [tox]
 envlist =
-   py38
+   clean
+   lint
    py39
    py310
+   py311
+   report
 
 [testenv]
+description = run tests
+package_root =
+   ./
+   plugins
 deps =
    pytest
    pytest-cov
    pytest-randomly
+   hypothesis
+   ; installes editable, packaged would be better:
+   -r requirements.txt
+   ; would work if extra would be public:
+   ; extras = plugins   
 commands =
-    pytest --cov=kimmdy --randomly-seed=1
+   pytest -m "not slow" --durations=15 --cov=kimmdy --randomly-seed=1 
+   ; pytest --cov=kimmdy --randomly-seed=1
+   ; pytest --cov=kimmdy --cov-append --randomly-seed=1
+   ; only test discovery:
+   ; pytest --cov=kimmdy --randomly-seed=1 --co   
+
+[testenv:lint]
+description = run black
+skip_install = true
+deps =
+   black
+commands = 
+   black src tests
+
+[testenv:clean]
+deps = coverage
+skip_install = true
+commands = coverage erase
+
+[testenv:report]
+deps = coverage
+skip_install = true
+commands =
+   coverage report
+   coverage html
+