Merge branch 'master' into ci/codecov

Author: oesteban

.circleci/config.yml

@@ -6,7 +6,7 @@ orbs:
 jobs:
   tests:
     docker:
-      - image: cimg/python:3.9
+      - image: cimg/python:3.11
         auth:
           username: $DOCKER_USER
           password: $DOCKER_PAT
@@ -24,18 +24,18 @@ jobs:
 
       - restore_cache:
           keys:
-            - deps-v10-{{ checksum "/tmp/src/templateflow/dev-requirements.txt"}}-{{ epoch }}
-            - deps-v10-{{ checksum "/tmp/src/templateflow/dev-requirements.txt"}}-
-            - deps-v10-
+            - deps-v11-{{ checksum "/tmp/src/templateflow/dev-requirements.txt"}}-{{ epoch }}
+            - deps-v11-{{ checksum "/tmp/src/templateflow/dev-requirements.txt"}}-
+            - deps-v11-
       - run:
           name: Prepare environment
           command: |
             python -m venv /tmp/venv
             source /tmp/venv/bin/activate
-            pip install -U pip
-            pip install -r /tmp/src/templateflow/dev-requirements.txt
-            pip install datalad
-            pip install -U build hatch hatchling nipreps-versions build twine
+            python -m pip install -U pip
+            python -m pip install -r /tmp/src/templateflow/dev-requirements.txt
+            python -m pip install -U "datalad ~= 0.19.0"
+            python -m pip install -U build hatch twine pkginfo
 
       - run:
           name: Install git and git-annex
@@ -54,11 +54,19 @@ jobs:
             git config --global user.email "[email protected]"
 
       - save_cache:
-          key: deps-v10-{{ checksum "/tmp/src/templateflow/requirements.txt"}}-{{ epoch }}
+          key: deps-v11-{{ checksum "/tmp/src/templateflow/dev-requirements.txt"}}-{{ epoch }}
           paths:
             - "/tmp/cache"
             - "/tmp/venv"
 
+      - run:
+          name: Test packaging
+          command: |
+            source /tmp/venv/bin/activate
+            cd /tmp/src/templateflow
+            python -m build
+            python -m twine check dist/*
+
       - run:
           name: Run tests (w/ DataLad)
           command: |
@@ -116,14 +124,6 @@ jobs:
       - store_test_results:
           path: /tmp/tests
 
-      - run:
-          name: Test packaging
-          command: |
-            source /tmp/venv/bin/activate
-            cd /tmp/src/templateflow
-            python -m build
-            twine check dist/*
-
   build_docs:
     machine:
       # https://discuss.circleci.com/t/linux-machine-executor-images-2021-april-q2-update/39928
@@ -186,20 +186,25 @@ jobs:
       - checkout:
           path: /tmp/src/templateflow
 
+      - run:
+          name: Generate requirements.txt
+          command: |
+            python /tmp/src/templateflow/.maint/update_requirements.py
+
       - restore_cache:
           keys:
-            - deps-v10-{{ checksum "/tmp/src/templateflow/requirements.txt"}}-{{ epoch }}
-            - deps-v10-{{ checksum "/tmp/src/templateflow/requirements.txt"}}-
-            - deps-v10-
+            - deps-v11-{{ checksum "/tmp/src/templateflow/dev-requirements.txt"}}-{{ epoch }}
+            - deps-v11-{{ checksum "/tmp/src/templateflow/dev-requirements.txt"}}-
+            - deps-v11-
 
       - run:
           name: Deploy to PyPi
           command: |
             source /tmp/venv/bin/activate
-            pip install build twine
+            python -m pip install build -U twine pkginfo
             python -m build
-            twine check dist/*
-            twine upload dist/*
+            python -m twine check dist/*
+            python -m twine upload dist/*
 
 workflows:
   version: 2

.github/workflows/pythonpackage.yml

@@ -49,7 +49,7 @@ jobs:
         run: |
           python -m venv /tmp/buildenv
           source /tmp/buildenv/bin/activate
-          python -m pip install -U build hatch hatchling nipreps-versions
+          python -m pip install -U build hatch
           if [[ "$GITHUB_REF" == refs/tags/* ]]; then
             TAG=${GITHUB_REF##*/}
           fi

CHANGES.rst

@@ -1,3 +1,16 @@
+24.2.0 (March 18, 2024)
+=======================
+Minor release including a new command line interface for the Client.
+
+* ENH: Add a command line interface (#123)
+* MAINT: Generate a requirements file with ``test`` dependencies (#125)
+* MAINT: Add codespell and make it fix some typos (#121)
+* MAINT: Revise code style according to ruff (#124)
+* MAINT: Add license header in all Python files (#122)
+* MAINT: Migrate to hatchling packaging (#120)
+* MAINT: Run ruff and address some issues (#119)
+* MAINT: Finalize migration of package build to PEP517/8 (#117)
+
 24.1.0 (March 15, 2024)
 =======================
 Minor release updating *PyBIDS*'s configuration to enable new entities

MANIFEST.in

@@ -43,7 +43,7 @@ test = [
     "coverage",
 ]
 datalad = [
-    "datalad ~= 0.12.0"
+    "datalad ~= 0.19.0"
 ]
 doc = [
     "nbsphinx",

pyproject.toml

@@ -28,6 +28,16 @@
 from templateflow import conf as tfc
 
 
+def _find_message(lines, msg, reverse=True):
+    if isinstance(lines, str):
+        lines = lines.splitlines()
+
+    for line in reversed(lines):
+        if line.strip().startswith(msg):
+            return True
+    return False
+
+
 @pytest.mark.parametrize('use_datalad', ['off', 'on'])
 def test_conf_init(monkeypatch, tmp_path, capsys, use_datalad):
     """Check the correct functioning of config set-up."""
@@ -56,53 +66,54 @@ def test_setup_home(monkeypatch, tmp_path, capsys, use_datalad):
     # First execution, the S3 stub is created (or datalad install)
     assert tfc.TF_CACHED is False
     assert tfc.setup_home() is False
-    out = capsys.readouterr()[0]
-    assert out.startswith('TemplateFlow was not cached')
+
+    out = capsys.readouterr().out
+    assert _find_message(out, 'TemplateFlow was not cached')
     assert ('TEMPLATEFLOW_HOME=%s' % home) in out
     assert home.exists()
     assert len(list(home.iterdir())) > 0
 
     updated = tfc.setup_home(force=True)  # Templateflow is now cached
     out = capsys.readouterr()[0]
-    assert not out.startswith('TemplateFlow was not cached')
+    assert _find_message(out, 'TemplateFlow was not cached') is False
 
     if use_datalad == 'on':
-        assert out.startswith('Updating TEMPLATEFLOW_HOME using DataLad')
+        assert _find_message(out, 'Updating TEMPLATEFLOW_HOME using DataLad')
         assert updated is True
 
     elif use_datalad == 'off':
         # At this point, S3 should be up-to-date
         assert updated is False
-        assert out.startswith('TEMPLATEFLOW_HOME directory (S3 type) was up-to-date.')
+        assert _find_message(out, 'TEMPLATEFLOW_HOME directory (S3 type) was up-to-date.')
 
         # Let's force an update
         rmtree(str(home / 'tpl-MNI152NLin2009cAsym'))
         updated = tfc.setup_home(force=True)
         out = capsys.readouterr()[0]
         assert updated is True
-        assert out.startswith('Updating TEMPLATEFLOW_HOME using S3.')
+        assert _find_message(out, 'Updating TEMPLATEFLOW_HOME using S3.')
 
     reload(tfc)
     assert tfc.TF_CACHED is True
     updated = tfc.setup_home()  # Templateflow is now cached
     out = capsys.readouterr()[0]
-    assert not out.startswith('TemplateFlow was not cached')
+    assert not _find_message(out, 'TemplateFlow was not cached')
 
     if use_datalad == 'on':
-        assert out.startswith('Updating TEMPLATEFLOW_HOME using DataLad')
+        assert _find_message(out, 'Updating TEMPLATEFLOW_HOME using DataLad')
         assert updated is True
 
     elif use_datalad == 'off':
         # At this point, S3 should be up-to-date
         assert updated is False
-        assert out.startswith('TEMPLATEFLOW_HOME directory (S3 type) was up-to-date.')
+        assert _find_message(out, 'TEMPLATEFLOW_HOME directory (S3 type) was up-to-date.')
 
         # Let's force an update
         rmtree(str(home / 'tpl-MNI152NLin2009cAsym'))
         updated = tfc.setup_home()
         out = capsys.readouterr()[0]
         assert updated is True
-        assert out.startswith('Updating TEMPLATEFLOW_HOME using S3.')
+        assert _find_message(out, 'Updating TEMPLATEFLOW_HOME using S3.')
 
 
 def test_layout(monkeypatch, tmp_path):