Merge branch 'main' into feat/track-test-test-cov

.github/workflows/gen-lock-file.yaml

@@ -8,15 +8,10 @@ defaults:
     shell: bash -leo pipefail {0}
 
 jobs:
-  create-conda-lock-file:
+  create-conda-lock-file-and-test-linux:
     runs-on: ubuntu-latest
     
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
-    
+    steps:  
     - name: Install conda-lock with Micromamba
       uses: mamba-org/setup-micromamba@v2
       with:
@@ -24,11 +19,16 @@ jobs:
         create-args: >-
           conda-lock
 
-    - name: Get Latest Version
+    # This saves me some time since we only need the latest tag
+    - name: Get latest tag
       id: latest-version
+      env:
+        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        REPO: ${{ github.repository }}
       run: |
-        LATEST_TAG=$(git describe --tags $(git rev-list --tags --max-count=1))
-        # slice off the v, ie v0.7.2 -> 0.7.2
+        LATEST_TAG=$(curl -s -H "Authorization: token $GH_TOKEN" \
+          https://api.github.com/repos/$REPO/tags \
+          | jq -r '.[0].name')
         VERSION=${LATEST_TAG:1}
         echo $VERSION
         echo "VERSION=$VERSION" >> $GITHUB_OUTPUT
@@ -52,15 +52,49 @@ jobs:
 
     - name: Generate lock files
       run: | 
-        conda lock --with-cuda 11.8 -f environment-to-lock.yaml openfe-conda-lock.yml 
+        conda lock --with-cuda 11.8 -f environment-to-lock.yaml --lockfile openfe-conda-lock.yml 
         cp openfe-conda-lock.yml openfe-${{ steps.latest-version.outputs.VERSION }}-conda-lock.yml
 
-    - name: Upload openfe forge to release
+    - name: Test lock file (linux)
+      run: |
+        conda-lock install -p /home/runner/micromamba/envs/lf-test openfe-conda-lock.yml
+        micromamba activate /home/runner/micromamba/envs/lf-test
+        openfe test
+
+    - name: Upload file as artifact
+      uses: actions/upload-artifact@v4
+      with:
+        name: conda-lock-files
+        path: "*conda-lock.yml"
+
+  test-osx-lock-file:
+    needs: create-conda-lock-file-and-test-linux
+    runs-on: macos-latest
+    steps:
+    - name: Download artifact
+      uses: actions/download-artifact@v4
+      with:
+        name: conda-lock-files
+
+    - name: Install conda-lock with Micromamba
+      uses: mamba-org/setup-micromamba@v2
+      with:
+        environment-name: conda-lock
+        create-args: >-
+          conda-lock
+
+    - name: Test lock file (osx)
+      run: |
+        conda-lock install -p /Users/runner/micromamba/envs/lf-test openfe-conda-lock.yml
+        micromamba activate /Users/runner/micromamba/envs/lf-test
+        openfe test
+
+    - name: Upload lock files to release
       uses: svenstaro/upload-release-action@v2
+      if: startsWith(github.ref, 'refs/tags/')
       with:
         repo_token: ${{ secrets.GITHUB_TOKEN }}
         file: "*conda-lock.yml"
         tag: ${{ github.ref }}
         overwrite: true
         file_glob: true
-      if: startsWith(github.ref, 'refs/tags/')

environment.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
 dependencies:
   - cinnabar ~=0.4.0
-  - click <8.2.0
+  - click >=8.2.0
   - coverage
   - duecredit<0.10
   - kartograf>=1.0.0

openfecli/tests/clicktypes/test_hyphenchoice.py

@@ -8,7 +8,7 @@ class TestHyphenAwareChoice:
     ])
     def test_init(self, value):
         ch = HyphenAwareChoice([value])
-        assert ch.choices == ["foo-bar-baz"]
+        assert ch.choices == ("foo-bar-baz",)
 
     @pytest.mark.parametrize('value', [
         "foo_bar_baz", "foo_bar-baz", "foo-bar_baz", "foo-bar-baz"

openfecli/tests/commands/test_gather.py

@@ -128,7 +128,7 @@ class TestResultLoading:
             assert "Missing ligand names and/or simulation type. Skipping" in captured.err
 
 def test_no_results_found():
-    runner = CliRunner(mix_stderr=False)
+    runner = CliRunner()
     cli_result = runner.invoke(gather, "not_a_file.txt")
     assert cli_result.exit_code == 1
     assert "No results JSON files found" in str(cli_result.stderr)
@@ -239,11 +239,11 @@ class TestGatherCMET:
     def test_cmet_full_results(self, cmet_result_dir, report, file_regression):
         results = [str(cmet_result_dir / f'results_{i}') for i in range(3)]
         args = ["--report", report]
-        runner = CliRunner(mix_stderr=False)
+        runner = CliRunner()
         cli_result = runner.invoke(gather, results + args + ['--tsv'])
 
         assert_click_success(cli_result)
-        file_regression.check(cli_result.output, extension='.tsv')
+        file_regression.check(cli_result.stdout, extension='.tsv')
 
     # TODO: add --allow-partial behavior checks
     @pytest.mark.parametrize('report', ["dg", "ddg", "raw"])
@@ -251,38 +251,38 @@ class TestGatherCMET:
         """Missing one complex replicate from one leg."""
         results = [str(cmet_result_dir / d) for d in ['results_0_partial', 'results_1', "results_2"]]
         args = ["--report", report]
-        runner = CliRunner(mix_stderr=False)
+        runner = CliRunner()
         cli_result = runner.invoke(gather, results + args + ['--tsv'])
 
         assert_click_success(cli_result)
-        file_regression.check(cli_result.output, extension='.tsv')
+        file_regression.check(cli_result.stdout, extension='.tsv')
 
     @pytest.mark.parametrize('report', ["dg", "ddg", "raw"])
     def test_cmet_missing_edge(self, cmet_result_dir, report,file_regression):
         results = [str(cmet_result_dir / f'results_{i}_remove_edge') for i in range(3)]
         args = ["--report", report]
-        runner = CliRunner(mix_stderr=False)
+        runner = CliRunner()
         cli_result = runner.invoke(gather, results + args + ['--tsv'])
-        file_regression.check(cli_result.output, extension='.tsv')
+        file_regression.check(cli_result.stdout, extension='.tsv')
 
         assert_click_success(cli_result)
-        file_regression.check(cli_result.output, extension='.tsv')
+        file_regression.check(cli_result.stdout, extension='.tsv')
 
     @pytest.mark.parametrize('report', ["ddg", "raw"])
     def test_cmet_failed_edge(self, cmet_result_dir, report, file_regression):
         results = [str(cmet_result_dir / f'results_{i}_failed_edge') for i in range(3)]
         args = ["--report", report]
-        runner = CliRunner(mix_stderr=False)
+        runner = CliRunner()
         cli_result = runner.invoke(gather, results + args + ['--tsv'])
 
         assert_click_success(cli_result)
-        file_regression.check(cli_result.output, extension=".tsv")
+        file_regression.check(cli_result.stdout, extension=".tsv")
 
     @pytest.mark.parametrize("allow_partial", [True, False])
     def test_cmet_too_few_edges_error(self, cmet_result_dir, allow_partial):
         results = [str(cmet_result_dir / f"results_{i}_failed_edge") for i in range(3)]
         args = ["--report", "dg"]
-        runner = CliRunner(mix_stderr=False)
+        runner = CliRunner()
         if allow_partial:
             args += ['--allow-partial']
 
@@ -298,41 +298,41 @@ class TestGatherCMET:
         """Missing one complex replicate from one leg."""
         results = glob.glob(f"{cmet_result_dir}/results_*/*solvent*", recursive=True)
         args = ["--report", report]
-        runner = CliRunner(mix_stderr=False)
+        runner = CliRunner()
         cli_result = runner.invoke(gather, results + args + ["-o", "-"])
 
         cli_result.exit_code == 1
-        file_regression.check(cli_result.output, extension='.tsv')
+        file_regression.check(cli_result.stdout, extension='.tsv')
 
     @pytest.mark.parametrize('report', ["ddg"])
     def test_cmet_missing_all_complex_legs_allow_partial(self, cmet_result_dir, report, file_regression):
         """Missing one complex replicate from one leg."""
         results = glob.glob(f"{cmet_result_dir}/results_*/*solvent*", recursive=True)
         args = ["--report", report, "--allow-partial"]
-        runner = CliRunner(mix_stderr=False)
+        runner = CliRunner()
         cli_result = runner.invoke(gather, results + args + ['--tsv'])
 
         assert_click_success(cli_result)
-        file_regression.check(cli_result.output, extension='.tsv')
+        file_regression.check(cli_result.stdout, extension='.tsv')
 
     @pytest.mark.parametrize('report', ["dg", "ddg", "raw"])
     def test_pretty_print(self, cmet_result_dir, report, file_regression):
         results = [str(cmet_result_dir / f'results_{i}') for i in range(3)]
         args = ["--report", report]
-        runner = CliRunner(mix_stderr=False)
+        runner = CliRunner()
         cli_result = runner.invoke(gather, results + args)
         assert_click_success(cli_result)
         # TODO: figure out how to mock terminal size, since it affects the table wrapping
-        # file_regression.check(cli_result.output, extension='.txt')
+        # file_regression.check(cli_result.stdout, extension='.txt')
 
     def test_write_to_file(self, cmet_result_dir):
-        runner = CliRunner(mix_stderr=False)
+        runner = CliRunner()
         with runner.isolated_filesystem():
             results = [str(cmet_result_dir / f'results_{i}') for i in range(3)]
             fname = "output.tsv"
             args = ["--report", "raw", "-o", fname]
             cli_result = runner.invoke(gather, results + args)
-            assert "writing raw output to 'output.tsv'" in cli_result.output
+            assert "writing raw output to 'output.tsv'" in cli_result.stdout
             assert pathlib.Path(fname).is_file()
 
 
@@ -348,7 +348,7 @@ def test_rbfe_gather(rbfe_result_dir, dataset, report, input_mode):
         "ddg": _RBFE_EXPECTED_DDG,
         "raw": _RBFE_EXPECTED_RAW,
     }[report]
-    runner = CliRunner(mix_stderr=False)
+    runner = CliRunner()
 
     if report:
         args = ["--report", report]
@@ -372,7 +372,7 @@ def test_rbfe_gather(rbfe_result_dir, dataset, report, input_mode):
 def test_rbfe_gather_single_repeats_dg_error(rbfe_result_dir):
     """A single repeat is insufficient for a dg calculation - should fail cleanly."""
 
-    runner = CliRunner(mix_stderr=False)
+    runner = CliRunner()
     results = rbfe_result_dir("rbfe_results_parallel_repeats")
     args = ['report','dg']
     cli_result = runner.invoke(gather, [f"{results}/replicate_0"] + args + ['--tsv'])
@@ -394,7 +394,7 @@ class TestRBFEGatherFailedEdges:
         return results_filtered
 
     def test_missing_leg_error(self, results_paths_serial_missing_legs: str):
-        runner = CliRunner(mix_stderr=False)
+        runner = CliRunner()
         result = runner.invoke(gather, results_paths_serial_missing_legs + ["--report", "dg"])
 
         assert result.exit_code == 1
@@ -405,7 +405,7 @@ class TestRBFEGatherFailedEdges:
 
 
     def test_missing_leg_allow_partial_disconnected(self, results_paths_serial_missing_legs: str):
-        runner = CliRunner(mix_stderr=False)
+        runner = CliRunner()
         with pytest.warns():
             args =  ["--report", "dg", "--allow-partial"]
             result = runner.invoke(gather, results_paths_serial_missing_legs + args + ['--tsv'])
@@ -414,7 +414,7 @@ class TestRBFEGatherFailedEdges:
 
 
     def test_missing_leg_allow_partial_(self, results_paths_serial_missing_legs: str):
-        runner = CliRunner(mix_stderr=False)
+        runner = CliRunner()
         # we *dont* want the suggestion to use --allow-partial if the user already used it!
         with pytest.warns(match='[^using the \-\-allow\-partial]'):
             args =  ["--report", "ddg", "--allow-partial"]