Merge pull request #92 from templateflow/fix/issue-86

FIX: Normalize extensions for leading dot & update doctests to new resources

Author: oesteban

.github/workflows/pythonpackage.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       matrix:
         python-version: [3.7, 3.8, 3.9]
-        pip: ["pip~=20.0", "pip~=21.0"]
+        pip: ["pip==21.2", "pip~=22.0"]
 
     steps:
     - uses: actions/checkout@v2
@@ -87,15 +87,15 @@ jobs:
         TEMPLATEFLOW_HOME: /tmp/home/sdist
       run: |
         source /tmp/install_sdist/bin/activate
-        python -m pip install /tmp/package/templateflow*.tar.gz
+        python -m pip install /tmp/package/templateflow*.tar.gz --force-reinstall
         find ${TEMPLATEFLOW_HOME} >> /tmp/.sdist-install.txt
     - name: Re-install in confined environment [sdist - missing template]
       env:
         TEMPLATEFLOW_HOME: /tmp/home/sdist
       run: |
         rm -rf ${TEMPLATEFLOW_HOME}/tpl-MNI152NLin2009cAsym
         source /tmp/install_sdist/bin/activate
-        python -m pip install /tmp/package/templateflow*.tar.gz
+        python -m pip install /tmp/package/templateflow*.tar.gz --force-reinstall
         python -c "import templateflow; templateflow.update(overwrite=False)"
         find ${TEMPLATEFLOW_HOME} >> /tmp/.sdist-install-2.txt
         diff /tmp/.sdist-install.txt /tmp/.sdist-install-2.txt
@@ -118,15 +118,15 @@ jobs:
         TEMPLATEFLOW_HOME: /tmp/home/wheel
       run: |
         source /tmp/install_wheel/bin/activate
-        python -m pip install /tmp/package/templateflow*.whl
+        python -m pip install /tmp/package/templateflow*.whl --force-reinstall
         find ${TEMPLATEFLOW_HOME} >> /tmp/.wheel-install.txt
     - name: Re-install in confined environment [wheel - missing template]
       env:
         TEMPLATEFLOW_HOME: /tmp/home/wheel
       run: |
         rm -rf ${TEMPLATEFLOW_HOME}/tpl-MNI152NLin2009cAsym
         source /tmp/install_wheel/bin/activate
-        python -m pip install /tmp/package/templateflow*.whl
+        python -m pip install /tmp/package/templateflow*.whl --force-reinstall
         # Wheels do not run post-install hooks:
         test ! -d ${TEMPLATEFLOW_HOME}/tpl-MNI152NLin2009cAsym
         python -c "import templateflow; templateflow.update(overwrite=False)"
@@ -142,6 +142,7 @@ jobs:
         source /tmp/setup_install/bin/activate
         python -m pip install -U "setuptools >= 45" wheel "setuptools_scm >= 6.2" \
                               setuptools_scm_git_archive "${{ matrix.pip }}"
+        python -m pip install "numpy==1.20" Cython "pandas==1.3" "scipy==1.7"
         python setup.py install
         INSTALLED_VERSION=$(python -c 'import templateflow as tf; print(tf.__version__, end="")')
         echo "INSTALLED: \"${INSTALLED_VERSION}\""
@@ -174,6 +175,7 @@ jobs:
         source /tmp/setup_develop/bin/activate
         python -m pip install -U "setuptools >= 45" wheel "setuptools_scm >= 6.2" \
                               setuptools_scm_git_archive "${{ matrix.pip }}"
+        python -m pip install "numpy==1.20" Cython "pandas==1.3" "scipy==1.7"
         python setup.py develop
         INSTALLED_VERSION=$(python -c 'import templateflow as tf; print(tf.__version__, end="")')
         echo "INSTALLED: \"${INSTALLED_VERSION}\""

templateflow/api.py

@@ -38,14 +38,14 @@ def get(template, raise_empty=False, **kwargs):
 
     Examples
     --------
-    >>> str(get('MNI152Lin', resolution=1, suffix='T1w'))  # doctest: +ELLIPSIS
+    >>> str(get('MNI152Lin', resolution=1, suffix='T1w', desc=None))  # doctest: +ELLIPSIS
     '.../tpl-MNI152Lin/tpl-MNI152Lin_res-01_T1w.nii.gz'
 
-    >>> str(get('MNI152Lin', resolution=2, suffix='T1w'))  # doctest: +ELLIPSIS
+    >>> str(get('MNI152Lin', resolution=2, suffix='T1w', desc=None))  # doctest: +ELLIPSIS
     '.../tpl-MNI152Lin/tpl-MNI152Lin_res-02_T1w.nii.gz'
 
     >>> [str(p) for p in get(
-    ...     'MNI152Lin', suffix='T1w')]  # doctest: +ELLIPSIS +NORMALIZE_WHITESPACE
+    ...     'MNI152Lin', suffix='T1w', desc=None)]  # doctest: +ELLIPSIS +NORMALIZE_WHITESPACE
     ['.../tpl-MNI152Lin/tpl-MNI152Lin_res-01_T1w.nii.gz',
      '.../tpl-MNI152Lin/tpl-MNI152Lin_res-02_T1w.nii.gz']
 
@@ -62,6 +62,10 @@ def get(template, raise_empty=False, **kwargs):
     ...
 
     """
+    # Normalize extensions to always have leading dot
+    if "extension" in kwargs:
+        kwargs["extension"] = _normalize_ext(kwargs["extension"])
+
     out_file = [
         Path(p) for p in TF_LAYOUT.get(template=template, return_type="file", **kwargs)
     ]
@@ -135,8 +139,8 @@ def templates(**kwargs):
     >>> all([t in tpls for t in base])
     True
 
-    >>> templates(suffix='PD')
-    ['MNI152Lin', 'MNI152NLin2009cAsym', 'MNI152NLin2009cSym', 'MNIInfant', 'MNIPediatricAsym']
+    >>> sorted(set(base).intersection(templates(suffix='PD')))
+    ['MNI152Lin', 'MNI152NLin2009cAsym']
 
     """
     return sorted(TF_LAYOUT.get_templates(**kwargs))
@@ -247,8 +251,7 @@ def _to_bibtex(doi, template, idx):
     import requests
 
     response = requests.post(
-        doi,
-        headers={"Accept": "application/x-bibtex; charset=utf-8"}
+        doi, headers={"Accept": "application/x-bibtex; charset=utf-8"}
     )
     if not response.ok:
         print(
@@ -258,3 +261,32 @@ def _to_bibtex(doi, template, idx):
         return doi
 
     return response.text
+
+
+def _normalize_ext(value):
+    """
+    Normalize extensions to have a leading dot.
+
+    Examples
+    --------
+    >>> _normalize_ext(".nii.gz")
+    '.nii.gz'
+    >>> _normalize_ext("nii.gz")
+    '.nii.gz'
+    >>> _normalize_ext(("nii", ".nii.gz"))
+    ['.nii', '.nii.gz']
+    >>> _normalize_ext(("", ".nii.gz"))
+    ['', '.nii.gz']
+    >>> _normalize_ext((None, ".nii.gz"))
+    [None, '.nii.gz']
+    >>> _normalize_ext([])
+    []
+
+    """
+
+    if not value:
+        return value
+
+    if isinstance(value, str):
+        return f"{'' if value.startswith('.') else '.'}{value}"
+    return [_normalize_ext(v) for v in value]

templateflow/tests/test_api.py

@@ -65,13 +65,26 @@
     "https://github.com/Washington-University/HCPpipelines/tree/master/global/templates"
 )
 
+fsaverage_fbib = """\
+@article{Fischl_1999,
+\tdoi = {10.1002/(sici)1097-0193(1999)8:4<272::aid-hbm10>3.0.co;2-4},
+\turl = {https://doi.org/10.1002%2F%28sici%291097-0193%281999%298%3A4%3C272%3A%3Aaid-hbm10%3E3.0.co%3B2-4},
+\tyear = 1999,
+\tpublisher = {Wiley},
+\tvolume = {8},
+\tnumber = {4},
+\tpages = {272--284},
+\tauthor = {Bruce Fischl and Martin I. Sereno and Roger B.H. Tootell and Anders M. Dale},
+\ttitle = {High-resolution intersubject averaging and a coordinate system for the cortical surface},
+\tjournal = {Human Brain Mapping}
+}"""
 
 @pytest.mark.parametrize(
     "template,urls,fbib,lbib",
     [
         ("MNI152NLin2009cAsym", mni2009_urls, mni2009_fbib, mni2009_lbib),
         ("fsLR", fslr_urls, fslr_fbib, fslr_lbib),
-        ("fsaverage", [], None, None),
+        ("fsaverage", ["https://doi.org/10.1002/(sici)1097-0193(1999)8:4%3C272::aid-hbm10%3E3.0.co;2-4"], fsaverage_fbib, None),
     ],
 )
 def test_citations(tmp_path, template, urls, fbib, lbib):
@@ -80,7 +93,7 @@ def test_citations(tmp_path, template, urls, fbib, lbib):
     bibs = api.get_citations(template, bibtex=True)
     if bibs:
         assert "".join(bibs[0]) == fbib
-        assert "".join(bibs[-1]) == lbib
+        assert len(bibs) == 1 if lbib is None else "".join(bibs[-1]) == lbib
     else:
         # no citations currently
-        assert template == "fsaverage"
+        assert False