🚧 start with GitHub Actions to ensure tests pass before larger refactor by enryH · Pull Request #10 · biosustain/croissance

enryH · 2026-01-26T16:07:38Z

update package metadata
add testing in GitHub Actions
make it ready for a PyPI release

- move information from setup.py to pyproject.toml - optional dependencies for tooling used

- test 1 - no result obtained at all - test 2 - wrong growth given

- to be updated using loc operator

enryH · 2026-01-27T13:53:50Z

With pandas three we will need to use .loc for integer indicies explicitly:

  /Users/heweb/Documents/repos/croissance/croissance/estimation/smoothing/segments.py:19: FutureWarning: The behavior of obj[i:j] with a float-dtype index is deprecated. In a future version, this will be treated as positional instead of label-based. For label-based slicing, use obj.loc[i:j] instead
    window = series[i : i + size * increment]
    
  /Users/heweb/Documents/repos/croissance/croissance/estimation/smoothing/segments.py:62: FutureWarning: The behavior of obj[i:j] with a float-dtype index is deprecated. In a future version, this will be treated as positional instead of label-based. For label-based slicing, use obj.loc[i:j] instead
    window = series[start:end]

Copilot

Pull request overview

This PR modernizes the project's build and CI/CD infrastructure by migrating from Travis CI to GitHub Actions, converting package metadata from setup.py to pyproject.toml, and refactoring tests to run independently without PDFWriter dependencies.

Changes:

Adds comprehensive GitHub Actions workflow with formatting checks (black, isort), linting (ruff), testing across Python versions, and automated PyPI publishing
Migrates package configuration from setup.py to pyproject.toml with setuptools_scm for version management
Splits monolithic test_process_curve_basic into three independent test functions (test_process_curve_basic0/1/2) and separates PDFWriter testing

Reviewed changes

Copilot reviewed 14 out of 15 changed files in this pull request and generated 13 comments.

Show a summary per file

File	Description
.github/workflows/cicd.yml	Adds new CI/CD pipeline with format, lint, test, build, and publish jobs
.github/workflows/README.md	Documents the CI/CD workflow structure and purpose
pyproject.toml	Migrates all package metadata, dependencies, and tooling configuration from setup.py
setup.py	Strips down to minimal setup() call with only find_packages()
tests/api_test.py	Refactors test_process_curve_basic into separate test functions and isolated PDFWriter test
.travis.yml	Removes deprecated Travis CI configuration
.gitignore	Expands with modern Python development patterns
croissance/*.py	Applies consistent import ordering per isort/black standards

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Copilot · 2026-01-27T14:07:40Z

.github/workflows/cicd.yml

+    if: startsWith(github.ref, 'refs/heads/main') || startsWith(github.ref, 'refs/tags')
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4


The build_source_dist and publish jobs use actions/checkout@v4 without specifying fetch-depth. When using setuptools_scm for version management, you may need full git history to correctly determine the version. Consider adding 'fetch-depth: 0' to the checkout action to ensure setuptools_scm has access to all tags and commit history.

Suggested change

- uses: actions/checkout@v4

- uses: actions/checkout@v4

with:

fetch-depth: 0

pyproject.toml

Copilot · 2026-01-27T14:07:41Z

.github/workflows/cicd.yml

+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"


Python version "3.10" should be quoted as a string. Without quotes, YAML interprets this as the float 3.1, which will cause the setup-python action to fail. Change to "3.10".

Copilot · 2026-01-27T14:07:41Z

.github/workflows/cicd.yml

+    runs-on: macos-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]


The test matrix only includes Python versions 3.11, 3.12, and 3.13, but pyproject.toml specifies requires-python = ">=3.9". This means Python 3.9 and 3.10 are supported but not tested. Either update the test matrix to include ["3.9", "3.10", "3.11", "3.12", "3.13"] or adjust the requires-python specification in pyproject.toml.

Copilot · 2026-01-27T14:07:42Z

pyproject.toml

+  "matplotlib>=1.4.3",
+  "numpy>=1.9.1",
+  "pandas>=0.18.0,<3.0.0",
+  "scipy>=0.14.0",


The dependency versions appear very old (matplotlib>=1.4.3 from 2015, numpy>=1.9.1 from 2014, pandas>=0.18.0 from 2016, scipy>=0.14.0 from 2014). These ancient versions may not be compatible with modern Python versions (3.9+). Consider updating the minimum versions to those compatible with Python 3.9+, or verify that these old versions actually work with the specified Python versions.

Suggested change

"matplotlib>=1.4.3",

"numpy>=1.9.1",

"pandas>=0.18.0,<3.0.0",

"scipy>=0.14.0",

"matplotlib>=3.3.0",

"numpy>=1.19.2",

"pandas>=1.2.0,<3.0.0",

"scipy>=1.5.0",

Copilot · 2026-01-27T14:07:42Z

tests/api_test.py

        result = process_curve(curve, constrain_n0=True, n0=0.0)

-        # self.assertAlmostEqual(mu, slope, 6, msg='growth rate (mu)={}'.format(mu))
+        # self.assertAlmostEqual(mu, slope, 6, msg="growth rate (mu)={}".format(mu))


The comment references "growth rate (mu)=" but uses the old Python 2 style .format() when there are no actual assertions or usage of this commented-out code. Since this is a commented line left from old unittest code (self.assertAlmostEqual), consider removing it entirely as it provides no value in its current state.

Copilot · 2026-01-27T14:07:43Z

tests/api_test.py

-        assert result.growth_phases[0].SNR > 1000
+    result = process_curve(curve, constrain_n0=True, n0=0.0)
+
+    # self.assertAlmostEqual(mu, slope, 6, msg="growth rate (mu)={}".format(mu))


The comment references "growth rate (mu)=" but uses the old Python 2 style .format() when there are no actual assertions or usage of this commented-out code. Since this is a commented line left from old unittest code (self.assertAlmostEqual), consider removing it entirely as it provides no value in its current state.

Copilot · 2026-01-27T14:07:43Z

tests/api_test.py

+def test_process_curve_basic0():
+    # with PDFWriter(Path("test.basic.pdf")) as doc:
+    mu = 0.5
+    pph = 4.0
+    curve = pandas.Series(
+        data=[numpy.exp(mu * i / pph) for i in range(100)],
+        index=[i / pph for i in range(100)],
+    )

-        result = process_curve(curve, constrain_n0=True, n0=0.0)
-        doc.write("#2 n0=0", result)
-        print(result.growth_phases)
-        assert len(result.growth_phases) == 1
-        assert mu == approx(result.growth_phases[0].slope, abs=1e-2)
-        assert 0.0 == approx(result.growth_phases[0].n0, 1e-6)
-        assert result.growth_phases[0].SNR > 1000
-
-        result = process_curve(curve, constrain_n0=False)
-        doc.write("#2 n0=auto", result)
-        assert len(result.growth_phases) == 1
-        assert mu == approx(result.growth_phases[0].slope, abs=1e-2)
-        assert -0.25 < result.growth_phases[0].n0 < 0.25
-        assert result.growth_phases[0].SNR > 1000
+    result = process_curve(curve, constrain_n0=True, n0=0.0)
+
+    # self.assertAlmostEqual(mu, slope, 6, msg="growth rate (mu)={}".format(mu))
+
+    # doc.write("#0 n0=1", result)
+    # print(result.growth_phases)
+    assert len(result.growth_phases) == 1
+    assert mu == approx(result.growth_phases[0].slope, abs=1e-2)
+    assert 0.0 == approx(result.growth_phases[0].n0, 1e-3)
+    assert result.growth_phases[0].SNR > 1000
+
+    result = process_curve(curve, constrain_n0=False)
+    # doc.write("#0 n0=auto", result)
+    # print(result.growth_phases)
+    assert len(result.growth_phases) == 1
+    assert mu == approx(result.growth_phases[0].slope, abs=1e-2)
+    assert -0.25 < result.growth_phases[0].n0 < 0.25
+    assert result.growth_phases[0].SNR > 1000
+
+
+def test_process_curve_basic1():
+
+    mu = 0.5
+    pph = 4.0
+
+    curve = pandas.Series(
+        data=(
+            [1.0] * 5
+            + [numpy.exp(mu * i / pph) for i in range(25)]
+            + [numpy.exp(mu * 24 / pph)] * 20
+        ),
+        index=([i / pph for i in range(50)]),
+    )
+
+    result = process_curve(curve, constrain_n0=True, n0=0.0)
+    # doc.write("#1 n0=0", result)
+    # print(result.growth_phases)
+    assert len(result.growth_phases) == 1
+    assert mu == approx(result.growth_phases[0].slope, abs=1e-2)
+    assert 0.0 == approx(result.growth_phases[0].n0, 1e-3)
+    assert result.growth_phases[0].SNR > 1000
+
+    result = process_curve(curve, constrain_n0=False)
+    # doc.write("#1 n0=auto", result)
+    # print(result.growth_phases)
+    assert len(result.growth_phases) == 1
+    assert mu == approx(result.growth_phases[0].slope, abs=1e-1)
+    assert -0.25 < result.growth_phases[0].n0 < 0.25
+    assert result.growth_phases[0].SNR > 1000
+
+
+def test_process_curve_basic2():


Test function names like test_process_curve_basic0, test_process_curve_basic1, and test_process_curve_basic2 are not descriptive. Consider using more meaningful names that describe what each test variant is testing, such as test_process_curve_exponential_only, test_process_curve_with_lag_and_stationary, and test_process_curve_with_linear_ramp. This would make test failures easier to understand.

Copilot · 2026-01-27T14:07:43Z

.github/workflows/cicd.yml

+
+  build_source_dist:
+    name: Build source distribution
+    if: startsWith(github.ref, 'refs/heads/main') || startsWith(github.ref, 'refs/tags')


The condition uses startsWith(github.ref, 'refs/heads/main') which will trigger builds on every push to main, not just on tags. Given that setuptools_scm derives version from git tags, building from non-tag commits on main may result in development versions. If the intent is to only build releases, consider removing the 'refs/heads/main' condition and only keeping 'refs/tags'.

Suggested change

if: startsWith(github.ref, 'refs/heads/main') || startsWith(github.ref, 'refs/tags')

if: startsWith(github.ref, 'refs/tags')

pyproject.toml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

enryH added 12 commits January 26, 2026 16:59

🚧 start with GitHub Actions to ensure tests pass before larger refactor

7afb85e

🔧 move to pyproject.toml so latest information can be added

580fd68

- move information from setup.py to pyproject.toml - optional dependencies for tooling used

🔥 delete old cdci tool file

701830e

🎨 format

4e3ae9b

🚧 make ruff basic checks pass

499f018

🎨 format

39d281b

:format: with latest stable black version

8824d9b

🚧 check if it works on mac images

7ffac9d

🎨 sort imports

bdee95e

🐛 two tests fail

3e89eec

- test 1 - no result obtained at all - test 2 - wrong growth given

🐛 pandas 3.0.0 changed accessing with integers

a678dce

- to be updated using loc operator

🎨 fix ruff complaints, test PDFWriter separately

a4b10c6

enryH requested review from Copilot and meono January 27, 2026 13:53

Copilot started reviewing on behalf of enryH January 27, 2026 13:55 View session

Copilot AI reviewed Jan 27, 2026

View reviewed changes

enryH marked this pull request as ready for review January 27, 2026 16:56

Apply suggestions from code review

402a512

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

enryH merged commit d1b809c into master Jan 29, 2026
7 checks passed

enryH deleted the cdci branch January 29, 2026 10:21

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🚧 start with GitHub Actions to ensure tests pass before larger refactor#10

🚧 start with GitHub Actions to ensure tests pass before larger refactor#10
enryH merged 13 commits intomasterfrom
cdci

enryH commented Jan 26, 2026 •

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	if: startsWith(github.ref, 'refs/heads/main') \|\| startsWith(github.ref, 'refs/tags')
	if: startsWith(github.ref, 'refs/tags')

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enryH commented Jan 26, 2026 •

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