Update hooks, cosmetics, current pytest-cookies (#136)

OpenSourceEconomics · Sep 15, 2023 · 5569b1f · 5569b1f
1 parent fabfb0f
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Showing 8 changed files with 38 additions and 33 deletions.
diff --git a/.gitignore b/.gitignore
@@ -65,3 +65,5 @@ ___*
 !.readthedocs.yml
 hooks.egg-info
 coverage.xml
+tmp*
+pytest-of-hmg
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,11 +3,11 @@ exclude: ^(\.|{{cookiecutter\.project_slug}})/.+
 repos:
   - repo: meta
     hooks:
-      # - id: check-hooks-apply  # Leave nbqa in here.
       - id: check-useless-excludes
+      # - id: check-hooks-apply  # Leave nbqa in here.
       # - id: identity  # Prints all files passed to pre-commits. Debugging.
   - repo: https://github.com/lyz-code/yamlfix
-    rev: 1.9.0
+    rev: 1.13.0
     hooks:
       - id: yamlfix
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -36,20 +36,20 @@ repos:
       - id: check-ast
       - id: check-docstring-first
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.30.0
+    rev: v1.32.0
     hooks:
       - id: yamllint
   - repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 23.9.1
     hooks:
       - id: black
         language_version: python3.11
   - repo: https://github.com/asottile/blacken-docs
-    rev: 1.13.0
+    rev: 1.16.0
     hooks:
       - id: blacken-docs
   - repo: https://github.com/PyCQA/docformatter
-    rev: v1.5.1
+    rev: v1.7.5
     hooks:
       - id: docformatter
         args:
@@ -60,7 +60,7 @@ repos:
           - '88'
           - --blank
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.259
+    rev: v0.0.289
     hooks:
       - id: ruff
       #   args:
@@ -73,26 +73,26 @@ repos:
           - --extra-keys
           - metadata.kernelspec metadata.language_info.version metadata.vscode
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.6.4
+    rev: 1.7.0
     hooks:
       - id: nbqa-black
       - id: nbqa-ruff
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.16
+    rev: 0.7.17
     hooks:
       - id: mdformat
         additional_dependencies: [mdformat-gfm, mdformat-black]
         args: [--wrap, '88']
         files: (README\.md)
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.16
+    rev: 0.7.17
     hooks:
       - id: mdformat
         additional_dependencies: [mdformat-myst, mdformat-black]
         args: [--wrap, '88']
         files: (docs/.)
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.4
+    rev: v2.2.5
     hooks:
       - id: codespell
         args: [--skip="**.ipynb"]

diff --git a/environment.yml b/environment.yml
@@ -20,6 +20,7 @@ dependencies:
   - pydata-sphinx-theme>=0.3.0
   - pytask>=0.2
   - pytest
+  - pytest-cookies
   - pytest-cov
   - python
   - setuptools_scm
@@ -30,6 +31,4 @@ dependencies:
   - sphinx-panels
   - sphinxcontrib-bibtex
   - toml
-  - pip:
-      - kaleido
-      - git+https://github.com/andriihomiak/pytest-cookies.git@fix/quotes_in_user_config
+  - pip: [kaleido]
diff --git a/pyproject.toml b/pyproject.toml
@@ -3,8 +3,10 @@ target-version = "py311"
 select = ["ALL"]
 fix = true
 extend-ignore = [
-    "PLR0133"  # Constants being compared, always happening with cookiecutter.
-]
+    "PLR0133",  # Constants being compared, always happening with cookiecutter.
+    "S603",  # `subprocess` call: check for execution of untrusted input
+    "S607",  # Starting a process with a partial executable path
+ ]
 exclude = [
     "docs/scripts"
 ]

diff --git a/{{cookiecutter.project_slug}}/.pre-commit-config.yaml b/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ repos:
       # - id: check-hooks-apply  # Leave nbqa in here.
       # - id: identity  # Prints all files passed to pre-commits. Debugging.
   - repo: https://github.com/lyz-code/yamlfix
-    rev: 1.9.0
+    rev: 1.13.0
     hooks:
       - id: yamlfix
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -33,20 +33,20 @@ repos:
       - id: check-ast
       - id: check-docstring-first{% if cookiecutter.add_linters == 'yes' %}
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.30.0
+    rev: v1.32.0
     hooks:
       - id: yamllint{% endif %}
   - repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 23.9.1
     hooks:
       - id: black
         language_version: python3.11
   - repo: https://github.com/asottile/blacken-docs
-    rev: 1.13.0
+    rev: 1.16.0
     hooks:
       - id: blacken-docs
   - repo: https://github.com/PyCQA/docformatter
-    rev: v1.5.1
+    rev: v1.7.5
     hooks:
       - id: docformatter
         args:
@@ -57,7 +57,7 @@ repos:
           - '88'
           - --blank
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.259
+    rev: v0.0.289
     hooks:
       - id: ruff
       #   args:
@@ -70,26 +70,29 @@ repos:
           - --extra-keys
           - metadata.kernelspec metadata.language_info.version metadata.vscode
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.6.4
+    rev: 1.7.0
     hooks:
       - id: nbqa-black
+        additional_dependencies: [black==23.9.1]
       - id: nbqa-ruff
+        additional_dependencies: [ruff==v0.0.289]
+        args: ['--ignore=B018,T201']
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.16
+    rev: 0.7.17
     hooks:
       - id: mdformat
         additional_dependencies: [mdformat-gfm, mdformat-black]
         args: [--wrap, '88']
         files: (README\.md)
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.16
+    rev: 0.7.17
     hooks:
       - id: mdformat
         additional_dependencies: [mdformat-myst, mdformat-black]
         args: [--wrap, '88']
         files: (docs/.)
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.4
+    rev: v2.2.5
     hooks:
       - id: codespell
         args: [--skip="**.ipynb"]

diff --git a/{{cookiecutter.project_slug}}/src/{{cookiecutter.project_slug}}/analysis/predict.py b/{{cookiecutter.project_slug}}/src/{{cookiecutter.project_slug}}/analysis/predict.py
@@ -39,5 +39,4 @@ def predict_prob_by_age(data, model, group):
         _new_data[group] = group_value
         predicted[group_value] = model.predict(_new_data)
 
-    predicted = pd.DataFrame(predicted)
-    return predicted
+    return pd.DataFrame(predicted)
diff --git a/{{cookiecutter.project_slug}}/tests/analysis/test_model.py b/{{cookiecutter.project_slug}}/tests/analysis/test_model.py
@@ -10,12 +10,12 @@
 
 @pytest.fixture()
 def data():
-    np.random.seed(0)
-    x = np.random.normal(size=100_000)
+    np.random.default_rng(seed=0)
+    x = np.random.Generator.normal(size=100_000)
     coef = 2.0
     prob = 1 / (1 + np.exp(-coef * x))
     return pd.DataFrame(
-        {"outcome_numerical": np.random.binomial(1, prob), "covariate": x},
+        {"outcome_numerical": np.random.Generator.binomial(1, prob), "covariate": x},
     )
 
 

diff --git a/{{cookiecutter.project_slug}}/tests/data_management/test_clean_data.py b/{{cookiecutter.project_slug}}/tests/data_management/test_clean_data.py
@@ -29,8 +29,8 @@ def test_clean_data_dropna(data, data_info):
 def test_clean_data_categorical_columns(data, data_info):
     data_clean = clean_data(data, data_info)
     for cat_col in data_info["categorical_columns"]:
-        cat_col = data_info["column_rename_mapping"].get(cat_col, cat_col)
-        assert data_clean[cat_col].dtype == "category"
+        renamed_col = data_info["column_rename_mapping"].get(cat_col, cat_col)
+        assert data_clean[renamed_col].dtype == "category"
 
 
 def test_clean_data_column_rename(data, data_info):