Fix pytest error (#26)

* Update example.archive.json

Fix pytest error. Schema expects a str expected instead of a bool.

* Add nomad-lab dependency to pyproject.toml

* Remove nomad-lab from github action

* Github action uses uv for dependency management now

* Update github actions

* Update github actions and uv dependency management

* Update Python versions in GitHub Actions workflow

* Replace deprecated function in EQEAnalyzer

* Update permissions in GitHub Actions workflow

* Update uv installation in GitHub Actions workflow

* Update Python version matrix in GitHub Actions workflow

* Add dependencies for nomad-schema-plugin-run and nomad-schema-plugin-simulation-workflow

.github/workflows/actions.yml

@@ -2,31 +2,44 @@ name: install-and-test-workflow
 
 on: [push]
 
+permissions:
+  contents: read
+
+env:
+  # using uv pip requires an existing venv by default
+  # allows installating packages in the system
+  UV_SYSTEM_PYTHON: true
+
 jobs:
   install-and-test:
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python_version: ["3.12", "3.11", "3.10", "3.9"]
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.9
+      - name: Set up Python ${{matrix.python_version}}
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: ${{matrix.python_version}}
+      - name: Install uv
+        run: |
+          curl -LsSf https://astral.sh/uv/install.sh | sh
+        # uses: astral-sh/setup-uv@v3
       - name: Install dependencies
         run: |
-          pip install --upgrade pip
-          # we need the latest nomad version for testing
-          pip install nomad-lab[infrastructure]@git+https://github.com/nomad-coe/nomad.git@develop
-          pip install '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
-          pip install coverage coveralls
+          uv pip install -e '.[dev]'
       - name: Test with pytest
         run: |
-          python -m coverage run -m pytest -sv
-      - name: Submit to coveralls
-        continue-on-error: true
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          coveralls --service=github
+          pytest
+      #     python -m coverage run -m pytest -sv
+      # - name: Submit to coveralls
+      #   continue-on-error: true
+      #   env:
+      #     GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      #   run: |
+      #     coveralls --service=github
       # - name: Test with nomad
       #   run: |
       #     python -m nomad.cli parse tests/data/example.archive.json
@@ -39,14 +52,14 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: 3.9
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
       - name: Build the package
         run: |
-          pip install --upgrade pip
-          pip install build
-          python -m build --sdist
+          uv build --sdist
       - name: Install the package
         run: |
-          pip install dist/*.tar.gz --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
+          uv pip install dist/*.tar.gz --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
       # - name: Test with nomad
       #   run: |
       #     python -m nomad.cli parse tests/data/example.archive.json

pyproject.toml

@@ -30,6 +30,9 @@ maintainers = [
     ]
 requires-python = ">=3.9"
 dependencies = [
+    "nomad-lab>=1.3.0",
+    "nomad-schema-plugin-run>=1.0.1",
+    "nomad-schema-plugin-simulation-workflow>=1.0.1",
     "rdkit",
     "openpyxl",
     "lxml_html_clean"
@@ -40,6 +43,9 @@ license = { file = "LICENSE" }
 "Homepage" = "https://github.com/FAIRmat-NFDI/nomad-perovskite-solar-cells-database"
 Repository = "https://github.com/FAIRmat-NFDI/nomad-perovskite-solar-cells-database"
 
+[tool.uv]
+index-url = "https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple"
+
 [project.optional-dependencies]
 dev = ["ruff", "pytest", "structlog"]
 

src/perovskite_solar_cell_database/data_tools/eqe_parser.py

@@ -266,7 +266,7 @@ def calculate_jsc(self):
         energy_AM15 = np.array(df_am15[df_am15.columns[1]])
         spectrum_AM15 = np.array(df_am15[df_am15.columns[2]])
         spectrum_AM15G_interp = np.interp(x, energy_AM15, spectrum_AM15)
-        jsc_calc = integrate.cumtrapz(y * spectrum_AM15G_interp, x)
+        jsc_calc = integrate.cumulative_trapezoid(y * spectrum_AM15G_interp, x)
         jsc = max(jsc_calc * q * 1e4)
         return jsc
 

tests/data/example.archive.json

@@ -73,7 +73,7 @@
             "composition_leadfree": false,
             "additives_compounds": "Cl",
             "band_gap": 1.6,
-            "band_gap_graded": false,
+            "band_gap_graded": "false",
             "band_gap_estimation_basis": "Composition",
             "storage_time_until_next_deposition_step": "Unknown",
             "storage_atmosphere": "Unknown"
@@ -255,4 +255,4 @@
             "irradiance_measured": false
         }
     }
-}
+}