Merge pull request #100 from Becksteinlab/update-build-system

update packaging and CI

Author: orbeckst

.codecov.yml

@@ -1,10 +1,14 @@
 # Codecov configuration to make it a bit less noisy
 coverage:
   status:
-    patch: false
+    patch:
+      default:
+        threshold: 1%
+        target: auto
     project:
       default:
-        threshold: 50%
+        threshold: 1%
+        target: auto
 comment:
   layout: "header"
   require_changes: false
@@ -13,7 +17,5 @@ comment:
   flags: null
   paths: null
 ignore:
-  - "imdclient/_version.py"
   - "imdclient/data"
   - "imdclient/tests"
-  - "examples"

CHANGELOG.md

@@ -15,6 +15,25 @@ The rules for this file:
     * YYYY-MM-DD date format (following ISO 8601)
   * accompany each entry with github issue/PR number (Issue #xyz)
 -->
+## [v0.2.1] - 2025-07-??
+### Authors
+@orbeckst
+
+### Changed
+* manual tests (tests/hpc_testing) were moved to docs/hpc_testing and are
+  not included in the packaged distribution (issue #98, PR #100)
+
+### Added
+
+### Fixed
+* updated license string in package metadata (issue #97)
+
+### Deprecated
+<!-- Soon-to-be removed features -->
+
+### Removed
+<!-- Removed features -->
+
 
 ## [v0.2.0] - 2025-07-18
 

devtools/conda-envs/test_env.yaml

@@ -1,24 +1,18 @@
 name: imdclient-test
 channels:
   - conda-forge
-  - defaults
 dependencies:
   # Base depends
   - python
   - pip
-
-  # MDAnalysis
-  - MDAnalysis
+  - numpy
 
   # Testing
   - pytest
   - pytest-cov
   - pytest-xdist
   - codecov
+  - MDAnalysis
   - MDAnalysisTests
   - docker-py
 
-  # Pip-only installs
-  # - pip:
-  #  - codecov
-

…ient/tests/hpc_testing/gromacs/README.md docs/hpc_testing/gromacs/README.mdimdclient/tests/hpc_testing/gromacs/README.md renamed to docs/hpc_testing/gromacs/README.md imdclient/tests/hpc_testing/gromacs/README.md renamed to docs/hpc_testing/gromacs/README.md

@@ -23,7 +23,7 @@ source activate imdclient-test
 
 Then, to run the tests, do:
 ```bash
-cd imdclient/tests/hpc_testing/gromacs
+cd docs/hpc_testing/gromacs
 chmod +x validate_gmx.sh
 
 ./validate_gmx.sh \
@@ -104,9 +104,9 @@ source activate imdclient-test
 
 mkdir tmp_test
 
-python imdclient/tests/test_manual.py \
-    --topol_arg imdclient/tests/hpc_testing/gromacs/struct.gro \
-    --traj_arg imdclient/tests/hpc_testing/gromacs/gmx_gpu_test.trr \
+python docs/hpc_testing/test_manual.py \
+    --topol_arg docs/hpc_testing/gromacs/struct.gro \
+    --traj_arg docs/hpc_testing/gromacs/gmx_gpu_test.trr \
     --first_frame_arg 0 \
     --tmp_path tmp_test
 ``` -->

…sts/hpc_testing/gromacs/gmx_gpu_test.mdp docs/hpc_testing/gromacs/gmx_gpu_test.mdpimdclient/tests/hpc_testing/gromacs/gmx_gpu_test.mdp renamed to docs/hpc_testing/gromacs/gmx_gpu_test.mdp imdclient/tests/hpc_testing/gromacs/gmx_gpu_test.mdp renamed to docs/hpc_testing/gromacs/gmx_gpu_test.mdp

@@ -23,7 +23,7 @@ source activate imdclient-test
 
 Then, to run the tests, do:
 ```bash
-cd imdclient/tests/hpc_testing/lammps
+cd docs/hpc_testing/lammps
 chmod +x validate_lmp.sh
 
 ./validate_lmp.sh \