Merge branch 'master' into enh-codespell

Author: oesteban

.circleci/config.yml

@@ -31,7 +31,7 @@ jobs:
             pip install -U pip
             pip install -r /tmp/src/templateflow/requirements.txt
             pip install datalad
-            pip install "setuptools>=45" "setuptools_scm >= 6.2" nipreps-versions build twine codecov
+            pip install -U build hatch hatchling nipreps-versions build twine codecov
 
       - run:
           name: Install git and git-annex
@@ -173,8 +173,8 @@ jobs:
           name: Build only this commit
           command: |
             export PATH="$HOME/.conda/bin:$PATH"
-            python -m pip install "setuptools_scm>=8"
-            python -m setuptools_scm
+            python -m pip install -U build hatch hatchling
+            python -m hatch version
             make -C docs SPHINXOPTS="-W" BUILDDIR="$HOME/html" CURBRANCH="${CIRCLE_TAG}" html
       - store_artifacts:
           path: ~/html

.git_archival.txt

@@ -1 +1,4 @@
-ref-names: $Format:%D$
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

.github/workflows/pythonpackage.yml

@@ -49,11 +49,11 @@ jobs:
         run: |
           python -m venv /tmp/buildenv
           source /tmp/buildenv/bin/activate
-          python -m pip install --upgrade setuptools setuptools_scm nipreps-versions
+          python -m pip install -U build hatch hatchling nipreps-versions
           if [[ "$GITHUB_REF" == refs/tags/* ]]; then
             TAG=${GITHUB_REF##*/}
           fi
-          THISVERSION=$( python -m setuptools_scm )
+          THISVERSION=$( python -m hatch version | tail -n1 | xargs )
           THISVERSION=${TAG:-$THISVERSION}
           echo "Expected VERSION: \"${THISVERSION}\""
           echo "version=${THISVERSION}" >> $GITHUB_OUTPUT

.gitignore

@@ -1,5 +1,5 @@
-# setuptools_scm
-templateflow/_version.py
+# hatchling
+_version.py
 
 # circleci hash checking
 requirements.txt

docs/api.rst

@@ -4,5 +4,6 @@ Information on specific functions, classes, and methods.
 
 .. toctree::
 
+   api/templateflow.cli
    api/templateflow.api
    api/templateflow.conf

docs/cli.rst

@@ -0,0 +1,15 @@
+Using the client with the Command-line interface (CLI)
+======================================================
+
+.. click:: templateflow.cli:main
+  :prog: templateflow
+  :nested: full
+
+Examples
+--------
+Listing all the compressed NIfTI files in ``fsaverage``::
+
+	$ templateflow ls fsaverage -x .nii.gz
+	~/.cache/templateflow/tpl-fsaverage/tpl-fsaverage_res-01_den-41k_T1w.nii.gz
+	~/.cache/templateflow/tpl-fsaverage/tpl-fsaverage_res-01_desc-brain_mask.nii.gz
+	~/.cache/templateflow/tpl-fsaverage/tpl-fsaverage_res-01_T1w.nii.gz

docs/conf.py

@@ -11,12 +11,13 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 from packaging.version import Version
-from templateflow import __version__, __copyright__, __packagename__
+
+from templateflow import __copyright__, __packagename__, __version__
 
 # -- Project information -----------------------------------------------------
 project = __packagename__
 copyright = __copyright__
-author = "The TemplateFlow Developers"
+author = 'The NiPreps Developers'
 
 # The full version, including alpha/beta/rc tags
 release = __version__
@@ -29,30 +30,31 @@
 
 # -- General configuration ---------------------------------------------------
 extensions = [
-    "sphinx.ext.autodoc",
-    "sphinx.ext.coverage",
-    "sphinx.ext.doctest",
-    "sphinx.ext.githubpages",
-    "sphinx.ext.ifconfig",
-    "sphinx.ext.intersphinx",
-    "sphinx.ext.mathjax",
-    "sphinx.ext.napoleon",
-    "sphinx.ext.viewcode",
-    "sphinxcontrib.apidoc",
-    "nbsphinx",
+    'sphinx.ext.autodoc',
+    'sphinx.ext.coverage',
+    'sphinx.ext.doctest',
+    'sphinx.ext.githubpages',
+    'sphinx.ext.ifconfig',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.viewcode',
+    'sphinxcontrib.apidoc',
+    'nbsphinx',
+    'sphinx_click',
 ]
 
 autodoc_mock_imports = [
-    "matplotlib",
-    "nilearn",
-    "nipy",
-    "nitime",
-    "numpy",
-    "pandas",
-    "seaborn",
-    "skimage",
-    "svgutils",
-    "transforms3d",
+    'matplotlib',
+    'nilearn',
+    'nipy',
+    'nitime',
+    'numpy',
+    'pandas',
+    'seaborn',
+    'skimage',
+    'svgutils',
+    'transforms3d',
 ]
 autodoc_autoreload = True
 
@@ -67,16 +69,16 @@
 # ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ["_templates"]
+templates_path = ['_templates']
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = ".rst"
+source_suffix = '.rst'
 
 # The master toctree document.
-master_doc = "index"
+master_doc = 'index'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -89,11 +91,11 @@
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = [
-    "_build",
-    "Thumbs.db",
-    ".DS_Store",
-    "api/modules.rst",
-    "api/templateflow.rst",
+    '_build',
+    'Thumbs.db',
+    '.DS_Store',
+    'api/modules.rst',
+    'api/templateflow.rst',
 ]
 
 # The name of the Pygments (syntax highlighting) style to use.
@@ -105,7 +107,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = "sphinx_rtd_theme"
+html_theme = 'sphinx_rtd_theme'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -116,7 +118,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["_static"]
+html_static_path = ['_static']
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -132,7 +134,7 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = "templateflowdoc"
+htmlhelp_basename = 'templateflowdoc'
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -158,10 +160,10 @@
 latex_documents = [
     (
         master_doc,
-        "templateflow.tex",
-        "TemplateFlow Documentation",
-        "The TemplateFlow Developers",
-        "manual",
+        'templateflow.tex',
+        'TemplateFlow Documentation',
+        'The TemplateFlow Developers',
+        'manual',
     ),
 ]
 
@@ -170,7 +172,7 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, "templateflow", "TemplateFlow Documentation", [author], 1)]
+man_pages = [(master_doc, 'templateflow', 'TemplateFlow Documentation', [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -181,12 +183,12 @@
 texinfo_documents = [
     (
         master_doc,
-        "templateflow",
-        "TemplateFlow Documentation",
+        'templateflow',
+        'TemplateFlow Documentation',
         author,
-        "TemplateFlow",
-        "One line description of project.",
-        "Miscellaneous",
+        'TemplateFlow',
+        'One line description of project.',
+        'Miscellaneous',
     ),
 ]
 
@@ -206,38 +208,38 @@
 # epub_uid = ''
 
 # A list of files that should not be packed into the epub file.
-epub_exclude_files = ["search.html"]
+epub_exclude_files = ['search.html']
 
 
 # -- Extension configuration -------------------------------------------------
 
-apidoc_module_dir = "../templateflow"
-apidoc_output_dir = "api"
+apidoc_module_dir = '../templateflow'
+apidoc_output_dir = 'api'
 apidoc_excluded_paths = [
-    "conftest.py",
-    "*/tests/*",
-    "tests/*",
-    "data/*",
+    'conftest.py',
+    '*/tests/*',
+    'tests/*',
+    'data/*',
 ]
 apidoc_separate_modules = True
-apidoc_extra_args = ["--module-first", "-d 1", "-T"]
+apidoc_extra_args = ['--module-first', '-d 1', '-T']
 
 # -- Options for intersphinx extension ---------------------------------------
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
-    "bids": ("https://bids-standard.github.io/pybids/", None),
-    "matplotlib": ("https://matplotlib.org/", None),
-    "nibabel": ("https://nipy.org/nibabel/", None),
-    "nipype": ("https://nipype.readthedocs.io/en/latest/", None),
-    "numpy": ("https://numpy.org/doc/stable/", None),
-    "pandas": ("http://pandas.pydata.org/pandas-docs/dev", None),
-    "python": ("https://docs.python.org/3/", None),
-    "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
+    'bids': ('https://bids-standard.github.io/pybids/', None),
+    'matplotlib': ('https://matplotlib.org/', None),
+    'nibabel': ('https://nipy.org/nibabel/', None),
+    'nipype': ('https://nipype.readthedocs.io/en/latest/', None),
+    'numpy': ('https://numpy.org/doc/stable/', None),
+    'pandas': ('http://pandas.pydata.org/pandas-docs/dev', None),
+    'python': ('https://docs.python.org/3/', None),
+    'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
 }
 
 # -- Options for versioning extension ----------------------------------------
-smv_branch_whitelist = r"^master$"
-smv_tag_whitelist = r"^\d+\.\d+\.\d+(?!rc|dev).*$"
+smv_branch_whitelist = r'^master$'
+smv_tag_whitelist = r'^\d+\.\d+\.\d+(?!rc|dev).*$'
 smv_released_pattern = r'^tags/.*$'
 smv_rebuild_tags = False

docs/environment.yml

@@ -151,7 +151,6 @@ dependencies:
   - readline=8.1=h46c0cb4_0
   - requests=2.27.1=pyhd8ed1ab_0
   - scipy=1.8.0=py39hee8e79c_1
-  - setuptools=62.1.0=py39hf3d152e_0
   - six=1.16.0=pyh6c4a22f_0
   - snowballstemmer=2.2.0=pyhd8ed1ab_0
   - soupsieve=2.3.1=pyhd8ed1ab_0
@@ -203,5 +202,8 @@ dependencies:
     - nipreps-versions==1.0.3
     - pandas==1.4.2
     - pybids==0.15.2
-    - setuptools_scm==7.1.0
     - sqlalchemy==1.3.24
+    - hatchling
+    - hatch-vcs
+    - nipreps-versions
+    - sphinx-click

docs/index.rst

@@ -12,6 +12,7 @@ Contents
 
     installation
     examples
+    cli
     datalad
     api
     changes