fix pip check for optional dependencies (#405)

* fix pip check for optional dependencies

* install optional dependencies

* Update pipeline.yml

* add new line

* Update check.py

* Update pipeline.yml

* Update environment-mace.yml

Author: jan-janssen

.ci_support/check.py

@@ -0,0 +1,16 @@
+import tomlkit
+
+
+if __name__ == "__main__":
+    with open("pyproject.toml", "r") as f:
+        data = tomlkit.load(f)
+
+    lst = []
+    for sub_lst in data["project"]["optional-dependencies"].values():
+        for el in sub_lst:
+            lst.append(el)
+
+    data["project"]["dependencies"] += [el for el in set(lst) if not el.startswith("pwtools")]
+
+    with open("pyproject.toml", "w") as f:
+        f.writelines(tomlkit.dumps(data))

.ci_support/environment-mace.yml

@@ -2,3 +2,4 @@ channels:
 - conda-forge
 dependencies:
 - pymace =0.3.6
+- pytorch =2.5.1

.ci_support/environment-qe.yml

@@ -2,4 +2,4 @@ channels:
 - conda-forge
 dependencies:
 - qe =7.2
-- pwtools =1.2.3
+- pwtools =1.2.3

.github/workflows/pipeline.yml

@@ -134,18 +134,24 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Conda config
-      run: echo -e "channels:\n  - conda-forge\n" > .condarc
+      run: |
+        cp .ci_support/environment.yml environment.yml
+        tail --lines=+4 .ci_support/environment-lammps.yml >> environment.yml
+        tail --lines=+4 .ci_support/environment-gpaw.yml >> environment.yml
+        echo -e "channels:\n  - conda-forge\n" > .condarc
     - name: Setup Mambaforge
       uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: '3.12'
         miniforge-version: latest
         condarc-file: .condarc
-        environment-file: .ci_support/environment.yml
+        environment-file: environment.yml
     - name: Pip check
       shell: bash -l {0}
       run: |
-        pip install versioneer[toml]==0.29
+        pip install versioneer[toml]==0.29 tomlkit
+        python .ci_support/check.py
+        cat pyproject.toml
         pip install . --no-deps --no-build-isolation
         pip check