Numpy 2.0 + scipy + matplotlib pre-release workflow (#89)

* pin pytest to 8.0 and above

* move conftest.py to root and turn warnings into errors

* add workflow testing against numpy 2.0

* skip coverage

* fix config file used

* also install pip-pre scipy and matplotlib

* scikit-learn also for nilearn compatibility with numpy 2.0

* don't run nilearn tests on pip-pre

* run 3.9 and 3.12 on circle and 3.7 compat on gh

* fix workflow name

* fix: importorskip is not a mark decorator

* catch user warning

* fix deprecated readfp

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* ignore conftest in module discovery

* fix uninstall step of nilearn

* try again to rm nilearn

* fix module discovery logic

* fix numpy deprecation of np.NINF and np.trapz

* fix missed importorskip("nilearn")

* fix deprecation of find_module in module discovery logic

* fix compatibility trapz <-> trapezoid

* fix compatibility function

* add missed pytest.importorskip("nilearn")

* fix imports, drop pkg_utils entirely

* fix missed imports

* rm unused variable

* use relative imports and fix circular import and namespace

* revert version import

* close log file handler

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix missed importorskip("nilearn")

* fix codecov yml

* suppress sphinx gallery warning

* mv trapezoid_compat

* trigger ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.circleci/config.yml

@@ -15,14 +15,14 @@ orbs:
 # Define a job to be invoked later in a workflow.
 # See: https://circleci.com/docs/2.0/configuration-reference/#jobs
 jobs:
-  test37: # This is the name of the job, feel free to change it to better match what you're trying to do!
+  test39: # This is the name of the job, feel free to change it to better match what you're trying to do!
     # These next lines defines a Docker executors: https://circleci.com/docs/2.0/executor-types/
     # You can specify an image from Dockerhub or use one of the convenience images from CircleCI's Developer Hub
     # A list of available CircleCI Docker convenience images are available here: https://circleci.com/developer/images/image/cimg/python
     # The executor is the environment in which the steps below will be executed - below will use a python 3.6.14 container
     # Change the version below to your required version of python
     docker:
-      - image: cimg/python:3.7
+      - image: cimg/python:3.9
     working_directory: /tmp/src/nigsp
     resource_class: medium
     # Checkout the code as the first step. This is a dedicated CircleCI step.
@@ -58,9 +58,9 @@ jobs:
           paths:
             - src/coverage/.coverage.py37
 
-  test310:
+  test312:
     docker:
-      - image: cimg/python:3.10
+      - image: cimg/python:3.12
     working_directory: /tmp/src/nigsp
     resource_class: medium
     steps:
@@ -85,7 +85,7 @@ jobs:
 
   style_check:
     docker:
-      - image: cimg/python:3.7
+      - image: cimg/python:3.11
     working_directory: /tmp/src/nigsp
     resource_class: small
     steps:
@@ -105,7 +105,7 @@ jobs:
   merge_coverage:
     working_directory: /tmp/src/nigsp
     docker:
-      - image: cimg/python:3.10
+      - image: cimg/python:3.11
     resource_class: small
     steps:
       - attach_workspace:
@@ -133,13 +133,13 @@ workflows:
     # Inside the workflow, you define the jobs you want to run.
     jobs:
       - style_check
-      - test37:
+      - test39:
           requires:
             - style_check
-      - test310:
+      - test312:
           requires:
             - style_check
       - merge_coverage:
           requires:
-            - test37
-            - test310
+            - test39
+            - test312

.github/workflows/pytest.yaml

@@ -0,0 +1,84 @@
+name: pytest
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+on:  # yamllint disable-line rule:truthy
+  pull_request:
+  push:
+    branches: [main]
+  workflow_dispatch:
+  schedule:
+    - cron: '0 8 * * 1'
+
+jobs:
+  pytest-compat:
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.7"]
+    name: pip compat - py${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: 'x64'
+      - name: Install dependencies
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools
+          python -m pip install --progress-bar off .[all,style]
+          python -m pip install --progress-bar off pytest pytest-cov coverage
+      - name: Run pytest
+        run: pytest nigsp --cov=nigsp --cov-report=xml --cov-config=setup.cfg
+      - name: Upload to codecov
+        uses: codecov/codecov-action@v4
+        with:
+          files: ./coverage.xml
+          flags: unittests  # optional
+          name: codecov-umbrella  # optional
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true  # optional (default = false)
+  pytest-pip-pre:
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11"]
+    name: pip pre-release - py${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: 'x64'
+      - name: Install dependencies
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools
+          python -m pip install --progress-bar off .[test]
+          python -m pip install matplotlib
+          python -m pip install --progress-bar off --upgrade --no-deps --pre --only-binary :all: -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple --timeout=180 matplotlib
+          python -m pip install --progress-bar off --upgrade --pre --only-binary :all: -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple --timeout=180 numpy scipy
+          python -m pip uninstall -y nilearn
+      - name: Run pytest
+        run: pytest nigsp --cov=nigsp --cov-report=xml --cov-config=setup.cfg
+      - name: Upload to codecov
+        uses: codecov/codecov-action@v4
+        with:
+          files: ./coverage.xml
+          flags: unittests  # optional
+          name: codecov-umbrella  # optional
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true  # optional (default = false)

codecov.yml

@@ -1,10 +1,10 @@
 codecov:
   branch: master
   strict_yaml_branch: master
-  require_ci_to_pass: yes
+  require_ci_to_pass: true
   bot: "codecov-io"
   max_report_age: 48
-  disable_default_path_fixes: no
+  disable_default_path_fixes: false
 
 coverage:
   precision: 2
@@ -40,4 +40,4 @@ ignore:
 comment:
   layout: "reach,diff,flags,tree"
   behavior: default
-  require_changes: no
+  require_changes: false

docs/conf.py

@@ -89,6 +89,9 @@
 nitpicky = True
 nitpick_ignore = []
 
+# list of warning types to suppress
+suppress_warnings = ["config.cache"]
+
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for

nigsp/__init__.py

@@ -1,18 +1,16 @@
-"""Hopefully importing everything."""
-
-import pkgutil
-
+from . import (
+    blocks,
+    cli,
+    due,
+    io,
+    objects,
+    operations,
+    references,
+    utils,
+    viz,
+    workflow,
+)
 from ._version import get_versions
-from .operations import graph, laplacian, metrics, nifti, surrogates, timeseries
-
-SKIP_MODULES = ["tests"]
 
 __version__ = get_versions()["version"]
 del get_versions
-
-__all__ = []
-for loader, module_name, is_pkg in pkgutil.walk_packages(__path__):
-    if "tests" not in module_name:
-        __all__.append(module_name)
-        _module = loader.find_module(module_name).load_module(module_name)
-        globals()[module_name] = _module

nigsp/blocks.py

@@ -10,8 +10,8 @@
 
 import logging
 
-from nigsp import io, viz
-from nigsp.operations import nifti
+from . import io, viz
+from .operations import nifti
 
 LGR = logging.getLogger(__name__)
 

nigsp/cli/run.py

@@ -3,17 +3,15 @@
 
 import argparse
 
-from nigsp import __version__
+from .. import __version__
 
 
 def _get_parser():
-    """
-    Parse command line inputs for this function.
+    """Parse command line inputs for this function.
 
     Returns
     -------
     parser.parse_args() : argparse dict
-
     """
     parser = argparse.ArgumentParser(
         description=(
@@ -251,8 +249,7 @@ def _get_parser():
 if __name__ == "__main__":
     raise RuntimeError(
         "nigsp/cli/run.py should not be run directly;\n"
-        "Please `pip install` nigsp and use the "
-        "`nigsp` command"
+        "Please `pip install` nigsp and use the `nigsp` command."
     )
 
 

nigsp/tests/conftest.py → nigsp/conftest.py

@@ -1,13 +1,31 @@
-"""
-This configuration test module was taken from phys2bids.
-Credit to the original author(s) and to the phys2bids community.
-"""
+from __future__ import annotations  # c.f. PEP 563, PEP 649
 
 import os
 import ssl
+from typing import TYPE_CHECKING
 from urllib.request import urlretrieve
 
-import pytest
+from pytest import fixture
+
+if TYPE_CHECKING:
+    from pytest import Config
+
+
+def pytest_configure(config: Config) -> None:
+    """Configure pytest options."""
+    warnings_lines = r"""
+    error::
+    """
+    for warning_line in warnings_lines.split("\n"):
+        warning_line = warning_line.strip()
+        if warning_line and not warning_line.startswith("#"):
+            config.addinivalue_line("filterwarnings", warning_line)
+
+
+"""
+The following fetch_file and configuration test module was taken from phys2bids.
+Credit to the original author(s) and to the phys2bids community.
+"""
 
 
 def fetch_file(osf_id, path, filename):
@@ -48,37 +66,37 @@ def fetch_file(osf_id, path, filename):
     return full_path
 
 
-@pytest.fixture(scope="session")
+@fixture(scope="session")
 def testdir(tmp_path_factory):
     """Test path that will be used to download all files."""
     return tmp_path_factory.getbasetemp()
 
 
-@pytest.fixture
+@fixture(scope="function")
 def atlas(testdir):
     return fetch_file("h6nj7", testdir, "atlas.nii.gz")
 
 
-@pytest.fixture
+@fixture(scope="function")
 def atlastime(testdir):
     return fetch_file("ts6a8", testdir, "ats.nii.gz")
 
 
-@pytest.fixture
+@fixture(scope="function")
 def mean_fc(testdir):
     return fetch_file("jrg8d", testdir, "mean_fc_matlab.tsv")
 
 
-@pytest.fixture
+@fixture(scope="function")
 def sdi(testdir):
     return fetch_file("rs4dn", testdir, "SDI_matlab.tsv")
 
 
-@pytest.fixture
+@fixture(scope="function")
 def sc_mtx(testdir):
     return fetch_file("vwh75", testdir, "sc.mat")
 
 
-@pytest.fixture
+@fixture(scope="function")
 def timeseries(testdir):
     return fetch_file("ay8df", testdir, "func.mat")

nigsp/io.py

@@ -26,7 +26,7 @@
 
 import numpy as np
 
-from nigsp.utils import change_var_type
+from .utils import change_var_type
 
 EXT_1D = [".txt", ".csv", ".tsv", ".1d", ".par", ".tsv.gz", ".csv.gz"]
 EXT_MAT = [".mat"]

nigsp/objects.py

@@ -17,7 +17,7 @@
 import logging
 from copy import deepcopy
 
-from nigsp import operations
+from . import operations
 
 LGR = logging.getLogger(__name__)
 

nigsp/operations/__init__.py

@@ -11,7 +11,7 @@
 `nigsp.operations.sdi` or `nigsp.metrisc.sdi`.
 """
 
-# Import all operations.
+from . import graph, laplacian, metrics, nifti, surrogates, timeseries
 from .graph import nodestrength, zerocross
 from .laplacian import (
     compute_laplacian,

nigsp/operations/surrogates.py

@@ -431,7 +431,7 @@ def _pmf(x, n, p):
     if return_masked:
         LGR.info("Returning masked empirical data")
         stat_mask = np.ma.array(
-            data=surr[..., -1], mask=np.invert(stat_mask), fill_value=np.NINF
+            data=surr[..., -1], mask=np.invert(stat_mask), fill_value=-np.inf
         ).squeeze()
     else:
         LGR.info("Returning mask")