Add pre-commit and ruff config (#73)

Closes #72
PEtab-dev · Jul 1, 2024 · 0f34f23 · 0f34f23
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diff --git a/.ci_pip_reqs.txt b/.ci_pip_reqs.txt
@@ -1,4 +1,4 @@
 pytest
-flake8
+ruff
 git+https://github.com/PEtab-dev/libpetab-python@develop
 sympy>=1.12.1
diff --git a/.github/workflows/ci_tests.yml b/.github/workflows/ci_tests.yml
@@ -28,11 +28,10 @@ jobs:
       run: |
         python -m pip install --upgrade pip wheel
         pip install -e .
+        # uninstall, otherwise git+... installation from .ci_pip_reqs.txt won't do anything
         pip uninstall -y petab
         pip install -r .ci_pip_reqs.txt
+    - name: Check style
+      run: ruff check
     - name: Run tests
-      run: |
-        python -m flake8 \
-          --exclude=build,doc,tmp,_model.py,conversion_modified_pysb.py,conversion_pysb.py \
-          --extend-ignore=F403,F405
-        pytest test
+      run: pytest test
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,30 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+exclude: |
+    (?x)^(
+        petabtests/cases/.*\.(md|tsv)|
+        petabtests/cases/.*/_model\.py|
+        petabtests/cases/.*/conversion_modified_pysb\.py|
+        cases/.*
+    )$
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.6.0
+  hooks:
+  - id: check-added-large-files
+  - id: check-merge-conflict
+  - id: check-yaml
+    args: [--allow-multiple-documents]
+  - id: end-of-file-fixer
+  - id: trailing-whitespace
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.5.0
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args:
+        - --fix
+
+    # Run the formatter.
+    - id: ruff-format
diff --git a/README.md b/README.md
@@ -11,7 +11,7 @@ The PEtab test suite can be downloaded from GitHub via
 
     git clone https://github.com/petab-dev/petab_test_suite
 
-The test suite comes with all necessary files pregenerated. 
+The test suite comes with all necessary files pregenerated.
 In the [petabtests](petabtests) subdirectory, it contains a python module for
 generating the tests and evaluating results. This can be installed via
 
@@ -25,7 +25,7 @@ of enumerated tests.
 Each test contains a descriptive `wxyz.md` file, and a script file `wxyz.py`
 file that can be used to generate all problem and solution files for the test.
 The necessary files are in the same case-specific folder, starting with an
-underscore. 
+underscore.
 In each case folder, there is a file `_wxyz.yaml` containing the parameter
 estimation problem description, and a file `_wxyz_solution.yaml` containing
 information on the expected results: chi2 value, log-likelihood, simulation

diff --git a/petabtests/C.py b/petabtests/C.py
@@ -5,18 +5,18 @@
 # paths
 BASE_DIR = Path(__file__).parent
 
-CASES_DIR = BASE_DIR / 'cases'
+CASES_DIR = BASE_DIR / "cases"
 
-DEFAULT_SBML_FILE = BASE_DIR / 'conversion.xml'
-DEFAULT_PYSB_FILE = BASE_DIR / 'conversion_pysb.py'
+DEFAULT_SBML_FILE = BASE_DIR / "conversion.xml"
+DEFAULT_PYSB_FILE = BASE_DIR / "conversion_pysb.py"
 
 # constants
 
-LLH = 'llh'
-CHI2 = 'chi2'
-SIMULATION_DFS = 'simulation_dfs'
-SIMULATION_FILES = 'simulation_files'
+LLH = "llh"
+CHI2 = "chi2"
+SIMULATION_DFS = "simulation_dfs"
+SIMULATION_FILES = "simulation_files"
 
-TOL_SIMULATIONS = 'tol_simulations'
-TOL_CHI2 = 'tol_chi2'
-TOL_LLH = 'tol_llh'
+TOL_SIMULATIONS = "tol_simulations"
+TOL_CHI2 = "tol_chi2"
+TOL_LLH = "tol_llh"
diff --git a/petabtests/cases/v1.0.0/sbml/0001/0001.py b/petabtests/cases/v1.0.0/sbml/0001/0001.py
@@ -19,38 +19,48 @@
 
 # problem --------------------------------------------------------------------
 
-condition_df = pd.DataFrame(data={
-    CONDITION_ID: ['c0'],
-}).set_index([CONDITION_ID])
+condition_df = pd.DataFrame(
+    data={
+        CONDITION_ID: ["c0"],
+    }
+).set_index([CONDITION_ID])
 
-measurement_df = pd.DataFrame(data={
-    OBSERVABLE_ID: ['obs_a', 'obs_a'],
-    SIMULATION_CONDITION_ID: ['c0', 'c0'],
-    TIME: [0, 10],
-    MEASUREMENT: [0.7, 0.1]
-})
+measurement_df = pd.DataFrame(
+    data={
+        OBSERVABLE_ID: ["obs_a", "obs_a"],
+        SIMULATION_CONDITION_ID: ["c0", "c0"],
+        TIME: [0, 10],
+        MEASUREMENT: [0.7, 0.1],
+    }
+)
 
-observable_df = pd.DataFrame(data={
-    OBSERVABLE_ID: ['obs_a'],
-    OBSERVABLE_FORMULA: ['A'],
-    NOISE_FORMULA: [0.5]
-}).set_index([OBSERVABLE_ID])
+observable_df = pd.DataFrame(
+    data={
+        OBSERVABLE_ID: ["obs_a"],
+        OBSERVABLE_FORMULA: ["A"],
+        NOISE_FORMULA: [0.5],
+    }
+).set_index([OBSERVABLE_ID])
 
-parameter_df = pd.DataFrame(data={
-    PARAMETER_ID: ['a0', 'b0', 'k1', 'k2'],
-    PARAMETER_SCALE: [LIN] * 4,
-    LOWER_BOUND: [0] * 4,
-    UPPER_BOUND: [10] * 4,
-    NOMINAL_VALUE: [1, 0, 0.8, 0.6],
-    ESTIMATE: [1] * 4,
-}).set_index(PARAMETER_ID)
+parameter_df = pd.DataFrame(
+    data={
+        PARAMETER_ID: ["a0", "b0", "k1", "k2"],
+        PARAMETER_SCALE: [LIN] * 4,
+        LOWER_BOUND: [0] * 4,
+        UPPER_BOUND: [10] * 4,
+        NOMINAL_VALUE: [1, 0, 0.8, 0.6],
+        ESTIMATE: [1] * 4,
+    }
+).set_index(PARAMETER_ID)
 
 # solutions ------------------------------------------------------------------
 
 simulation_df = measurement_df.copy(deep=True).rename(
-    columns={MEASUREMENT: SIMULATION})
-simulation_df[SIMULATION] = [analytical_a(t, 1, 0, 0.8, 0.6)
-                             for t in simulation_df[TIME]]
+    columns={MEASUREMENT: SIMULATION}
+)
+simulation_df[SIMULATION] = [
+    analytical_a(t, 1, 0, 0.8, 0.6) for t in simulation_df[TIME]
+]
 
 
 case = PetabTestCase(

diff --git a/petabtests/cases/v1.0.0/sbml/0002/0002.py b/petabtests/cases/v1.0.0/sbml/0002/0002.py
@@ -25,42 +25,51 @@
 
 # problem --------------------------------------------------------------------
 
-condition_df = pd.DataFrame(data={
-    CONDITION_ID: ['c0', 'c1'],
-    'a0': [0.8, 0.9],
-    'b0': [nan, nan],
-}).set_index([CONDITION_ID])
-
-measurement_df = pd.DataFrame(data={
-    OBSERVABLE_ID: ['obs_a'] * 4,
-    SIMULATION_CONDITION_ID: ['c0', 'c0', 'c1', 'c1'],
-    TIME: [0, 10, 0, 10],
-    MEASUREMENT: [0.7, 0.1, 0.8, 0.2]
-})
-
-observable_df = pd.DataFrame(data={
-    OBSERVABLE_ID: ['obs_a'],
-    OBSERVABLE_FORMULA: ['A'],
-    NOISE_FORMULA: [1]
-}).set_index([OBSERVABLE_ID])
-
-parameter_df = pd.DataFrame(data={
-    PARAMETER_ID: ['k1', 'k2'],
-    PARAMETER_SCALE: [LIN] * 2,
-    LOWER_BOUND: [0] * 2,
-    UPPER_BOUND: [10] * 2,
-    NOMINAL_VALUE: [0.8, 0.6],
-    ESTIMATE: [1] * 2,
-}).set_index(PARAMETER_ID)
+condition_df = pd.DataFrame(
+    data={
+        CONDITION_ID: ["c0", "c1"],
+        "a0": [0.8, 0.9],
+        "b0": [nan, nan],
+    }
+).set_index([CONDITION_ID])
+
+measurement_df = pd.DataFrame(
+    data={
+        OBSERVABLE_ID: ["obs_a"] * 4,
+        SIMULATION_CONDITION_ID: ["c0", "c0", "c1", "c1"],
+        TIME: [0, 10, 0, 10],
+        MEASUREMENT: [0.7, 0.1, 0.8, 0.2],
+    }
+)
+
+observable_df = pd.DataFrame(
+    data={
+        OBSERVABLE_ID: ["obs_a"],
+        OBSERVABLE_FORMULA: ["A"],
+        NOISE_FORMULA: [1],
+    }
+).set_index([OBSERVABLE_ID])
+
+parameter_df = pd.DataFrame(
+    data={
+        PARAMETER_ID: ["k1", "k2"],
+        PARAMETER_SCALE: [LIN] * 2,
+        LOWER_BOUND: [0] * 2,
+        UPPER_BOUND: [10] * 2,
+        NOMINAL_VALUE: [0.8, 0.6],
+        ESTIMATE: [1] * 2,
+    }
+).set_index(PARAMETER_ID)
 
 # solutions ------------------------------------------------------------------
 
 simulation_df = measurement_df.copy(deep=True).rename(
-    columns={MEASUREMENT: SIMULATION})
-simulation_df[SIMULATION] = [*[analytical_a(t, 0.8, 1, 0.8, 0.6)
-                               for t in [0, 10]],
-                             *[analytical_a(t, 0.9, 1, 0.8, 0.6)
-                               for t in [0, 10]]]
+    columns={MEASUREMENT: SIMULATION}
+)
+simulation_df[SIMULATION] = [
+    *[analytical_a(t, 0.8, 1, 0.8, 0.6) for t in [0, 10]],
+    *[analytical_a(t, 0.9, 1, 0.8, 0.6) for t in [0, 10]],
+]
 
 case = PetabTestCase(
     id=2,

diff --git a/petabtests/cases/v1.0.0/sbml/0003/0003.py b/petabtests/cases/v1.0.0/sbml/0003/0003.py
@@ -25,45 +25,56 @@
 
 # problem --------------------------------------------------------------------
 
-condition_df = pd.DataFrame(data={
-    CONDITION_ID: ['c0'],
-}).set_index([CONDITION_ID])
+condition_df = pd.DataFrame(
+    data={
+        CONDITION_ID: ["c0"],
+    }
+).set_index([CONDITION_ID])
 
-measurement_df = pd.DataFrame(data={
-    OBSERVABLE_ID: ['obs_a', 'obs_a'],
-    SIMULATION_CONDITION_ID: ['c0', 'c0'],
-    TIME: [0, 10],
-    MEASUREMENT: [0.7, 0.1],
-    OBSERVABLE_PARAMETERS: ['0.5;2', '0.5;2']
-})
+measurement_df = pd.DataFrame(
+    data={
+        OBSERVABLE_ID: ["obs_a", "obs_a"],
+        SIMULATION_CONDITION_ID: ["c0", "c0"],
+        TIME: [0, 10],
+        MEASUREMENT: [0.7, 0.1],
+        OBSERVABLE_PARAMETERS: ["0.5;2", "0.5;2"],
+    }
+)
 
-observable_df = pd.DataFrame(data={
-    OBSERVABLE_ID: ['obs_a'],
-    OBSERVABLE_FORMULA: ['observableParameter1_obs_a * A + '
-                         'observableParameter2_obs_a'],
-    NOISE_FORMULA: [0.5]
-}).set_index([OBSERVABLE_ID])
+observable_df = pd.DataFrame(
+    data={
+        OBSERVABLE_ID: ["obs_a"],
+        OBSERVABLE_FORMULA: [
+            "observableParameter1_obs_a * A + " "observableParameter2_obs_a"
+        ],
+        NOISE_FORMULA: [0.5],
+    }
+).set_index([OBSERVABLE_ID])
 
-parameter_df = pd.DataFrame(data={
-    PARAMETER_ID: ['a0', 'b0', 'k1', 'k2'],
-    PARAMETER_SCALE: [LIN] * 4,
-    LOWER_BOUND: [0] * 4,
-    UPPER_BOUND: [10] * 4,
-    NOMINAL_VALUE: [1, 0, 0.8, 0.6],
-    ESTIMATE: [1] * 4,
-}).set_index(PARAMETER_ID)
+parameter_df = pd.DataFrame(
+    data={
+        PARAMETER_ID: ["a0", "b0", "k1", "k2"],
+        PARAMETER_SCALE: [LIN] * 4,
+        LOWER_BOUND: [0] * 4,
+        UPPER_BOUND: [10] * 4,
+        NOMINAL_VALUE: [1, 0, 0.8, 0.6],
+        ESTIMATE: [1] * 4,
+    }
+).set_index(PARAMETER_ID)
 
 # solutions ------------------------------------------------------------------
 
 simulation_df = measurement_df.copy(deep=True).rename(
-    columns={MEASUREMENT: SIMULATION})
-simulation_df[SIMULATION] = [0.5 * analytical_a(t, 1, 0, 0.8, 0.6) + 2
-                             for t in simulation_df[TIME]]
+    columns={MEASUREMENT: SIMULATION}
+)
+simulation_df[SIMULATION] = [
+    0.5 * analytical_a(t, 1, 0, 0.8, 0.6) + 2 for t in simulation_df[TIME]
+]
 
 case = PetabTestCase(
     id=3,
     brief="Simulation. Numeric observable parameter overrides in measurement "
-          "table.",
+    "table.",
     description=DESCRIPTION,
     model=DEFAULT_SBML_FILE,
     condition_dfs=[condition_df],