Adopt ruff and pre-commit for linting and formatting (#139)

* linting and formatting with ruff

* configure pre-commit

* ignore notebooks

* pin jupyterlab

* rename step

* bump jupyter-bokeh

* bump codeql

.github/workflows/codeql.yml

@@ -27,15 +27,15 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v2
+        uses: github/codeql-action/init@v3
         with:
           languages: ${{ matrix.language }}
           queries: +security-and-quality
 
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v2
+        uses: github/codeql-action/autobuild@v3
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v2
+        uses: github/codeql-action/analyze@v3
         with:
           category: "/language:${{ matrix.language }}"

.github/workflows/main.yml

@@ -31,18 +31,13 @@ jobs:
       - name: Install and configure Poetry
         uses: snok/install-poetry@v1
         with:
-          version: 1.7.1
+          version: 1.8.2
           virtualenvs-create: true
           virtualenvs-in-project: true
       - name: Install dependencies
-        run: poetry install --with vis --no-interaction
-      - name: Lint with flake8
-        run: |
-          source $VENV
-          # stop the build if there are Python syntax errors or undefined names
-          flake8 mendeleev --count --select=E9,F63,F7,F82 --max-line-length=127 --show-source --statistics
-          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-          black --check mendeleev
+        run: poetry install --with vis --no-interaction -v
+      - name: Lint and format with ruff
+        uses: pre-commit/[email protected]
       - name: Test with pytest
         run: |
           source $VENV 

.pre-commit-config.yaml

@@ -0,0 +1,12 @@
+exclude: "^(alembic|notebooks)/"
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.3.3
+    hooks:
+      # Run the linter.
+      - id: ruff
+        types_or: [python, pyi, jupyter]
+      # Run the formatter.
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]

docs/source/api/mendeleev.cli.rst

@@ -0,0 +1,29 @@
+mendeleev.cli
+=============
+
+.. automodule:: mendeleev.cli
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      clielement
+
+
+
+
+
+
+
+
+
+
+
+
+

docs/source/api/mendeleev.db.rst

@@ -0,0 +1,31 @@
+mendeleev.db
+============
+
+.. automodule:: mendeleev.db
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      get_engine
+      get_package_dbpath
+      get_session
+
+
+
+
+
+
+
+
+
+
+
+
+

docs/source/api/mendeleev.econf.rst

@@ -0,0 +1,40 @@
+mendeleev.econf
+===============
+
+.. automodule:: mendeleev.econf
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      get_l
+      get_spin_strings
+      print_spin_occupations
+      shell_capactity
+      subshell_capacity
+      subshell_degeneracy
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      ElectronicConfiguration
+
+
+
+
+
+
+
+
+

docs/source/api/mendeleev.electronegativity.rst

@@ -0,0 +1,37 @@
+mendeleev.electronegativity
+===========================
+
+.. automodule:: mendeleev.electronegativity
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      allred_rochow
+      cottrell_sutton
+      generic
+      gordy
+      li_xue
+      martynov_batsanov
+      mulliken
+      nagle
+      sanderson
+
+
+
+
+
+
+
+
+
+
+
+
+

docs/source/api/mendeleev.fetch.rst

@@ -0,0 +1,36 @@
+mendeleev.fetch
+===============
+
+.. automodule:: mendeleev.fetch
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      add_plot_columns
+      fetch_electronegativities
+      fetch_ionic_radii
+      fetch_ionization_energies
+      fetch_neutral_data
+      fetch_table
+      get_app_data
+      get_zeff
+
+
+
+
+
+
+
+
+
+
+
+
+

docs/source/api/mendeleev.ion.rst

@@ -0,0 +1,29 @@
+mendeleev.ion
+=============
+
+.. automodule:: mendeleev.ion
+
+
+
+
+
+
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      Ion
+
+
+
+
+
+
+
+
+

docs/source/api/mendeleev.mendeleev.rst

@@ -0,0 +1,33 @@
+mendeleev.mendeleev
+===================
+
+.. automodule:: mendeleev.mendeleev
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      deltaN
+      element
+      get_all_elements
+      ids_to_attr
+      isotope
+
+
+
+
+
+
+
+
+
+
+
+
+

docs/source/api/mendeleev.models.rst

@@ -0,0 +1,46 @@
+mendeleev.models
+================
+
+.. automodule:: mendeleev.models
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      estimate_from_group
+      fetch_attrs_for_group
+      with_uncertainty
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      Element
+      Group
+      IonicRadius
+      IonizationEnergy
+      Isotope
+      IsotopeDecayMode
+      OxidationState
+      PhaseTransition
+      ScreeningConstant
+      Series
+
+
+
+
+
+
+
+
+

docs/source/api/mendeleev.utils.rst

@@ -0,0 +1,30 @@
+mendeleev.utils
+===============
+
+.. automodule:: mendeleev.utils
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      coeffs
+      n_effective
+
+
+
+
+
+
+
+
+
+
+
+
+