Merge branch 'add_PoreAnalyser_to_MDKits' of https://github.com/DSeif…

…erth/MDAKits into add_PoreAnalyser_to_MDKits
MDAnalysis · Oct 16, 2024 · 79fad3c · 79fad3c
2 parents 5f2cd3d + 37c3481
commit 79fad3c
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Showing 8 changed files with 14 additions and 10 deletions.
diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml
@@ -40,7 +40,7 @@ jobs:
     runs-on: ubuntu-latest
     outputs:
       python-stable: ${{ steps.get-compatible-python.outputs.stable-python }}
-      python-min: ${{ steps.get-compatible-python.outputs.oldest-pythons }}
+      python-min: ${{ steps.get-compatible-python.outputs.oldest-python }}
 
     steps:
       - uses: actions/setup-python@v4

diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml
@@ -44,7 +44,7 @@ jobs:
     runs-on: ubuntu-latest
     outputs:
       python-stable: ${{ steps.get-compatible-python.outputs.stable-python }}
-      python-min: ${{ steps.get-compatible-python.outputs.oldest-pythons }}
+      python-min: ${{ steps.get-compatible-python.outputs.oldest-python }}
     steps:
       - uses: actions/setup-python@v4
         with:

diff --git a/docs/source/reviewersguide.rst b/docs/source/reviewersguide.rst
@@ -206,6 +206,8 @@ is failing
 ``test_dependencies``: a list of commands for installing any dependencies required by the MDAKit’s tests.
 This is a *list of strings* (*AUTOMATIC CHECK*).
 
+- *note* : care should be taken to to override the underlying ``mamba`` environment. For example, this should _not_ attempt to do a ``mamba env update`` call as it will overwrite the base mamba environment and one ends up with a conda environment without the base mdakit dependencies.  
+
 
 
 *Optional* entries 

diff --git a/mdakits/lipyds/status.yaml b/mdakits/lipyds/status.yaml
@@ -11,7 +11,7 @@ develop:
   install_mdanalysis: true
   install_python: true
   install_test_deps: true
-  numfails: 60
+  numfails: 66
   run_tests: false
 latest:
   install_mdakit: true

diff --git a/mdakits/mda-tui/status.yaml b/mdakits/mda-tui/status.yaml
@@ -11,12 +11,12 @@ develop:
   install_mdanalysis: true
   install_python: true
   install_test_deps: true
-  numfails: 10
+  numfails: 16
   run_tests: false
 latest:
   install_mdakit: true
   install_mdanalysis: true
   install_python: true
   install_test_deps: true
-  numfails: 10
+  numfails: 16
   run_tests: false
diff --git a/mdakits/propkatraj/status.yaml b/mdakits/propkatraj/status.yaml
@@ -18,5 +18,5 @@ latest:
   install_mdanalysis: true
   install_python: true
   install_test_deps: true
-  numfails: 22
-  run_tests: false
+  numfails: 0
+  run_tests: true
diff --git a/mdakits/zarrtraj/metadata.yaml b/mdakits/zarrtraj/metadata.yaml
@@ -90,7 +90,7 @@ run_tests:
 ## The default below _might_ be sufficient or you might not even need MDAnalysisTests:
 ## make sure that it is appropriate for how you run tests.
 test_dependencies:
-  - mamba env update --file https://raw.githubusercontent.com/Becksteinlab/zarrtraj/main/devtools/conda-envs/test_env.yaml --name test
+  - mamba install "moto[server]>=5.0.3"
 
 ## str: the organisation name the MDAKit falls under
 project_org: Becksteinlab

diff --git a/utils/mdakit.py b/utils/mdakit.py
@@ -261,9 +261,11 @@ def get_matching_version(self, max_ver: str = "3.11", min_ver: str = "3.8",
 
         while (current_version.to_version() >= min_version.to_version()):
             for spec in pin_specifiers:
+                # Fetch the pin version string and convert it for comparison
+                pin_ver = version.TargetVersion.from_str(spec.version)
                 compatible_version = version._operators[spec.operator](
-                        current_version.to_string(),
-                        spec.version,
+                        current_version.to_version(),
+                        pin_ver.to_version(),
                 )
 
             if compatible_version: