Merge pull request #113 from templateflow/ci/manual-trigger

CI: Add manual trigger, bump action versions

.github/workflows/pythonpackage.yml

@@ -4,6 +4,7 @@
 name: Python package
 
 on:
+  workflow_dispatch:
   push:
     branches: [ master ]
     tags: [ '*' ]
@@ -23,13 +24,13 @@ jobs:
     outputs:
       version: ${{ steps.get_version.outputs.version }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-v1
@@ -39,7 +40,7 @@ jobs:
       - name: Build sdist and wheel
         run: python -m build
       - run: twine check dist/*
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: dist
           path: dist/
@@ -73,20 +74,20 @@ jobs:
       TEMPLATEFLOW_HOME: /tmp/home
       THISVERSION: ${{ needs.build.outputs.version }}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       if: matrix.mode == 'repo'  || matrix.mode == 'editable'
       with:
         fetch-depth: 0
-    - uses: actions/download-artifact@v3
+    - uses: actions/download-artifact@v4
       if: matrix.mode == 'sdist'  || matrix.mode == 'wheel'
       with:
         name: dist
         path: /tmp/package/
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - uses: actions/cache@v3
+    - uses: actions/cache@v4
       with:
         path: ~/.cache/pip
         key: pip-cache-v1

templateflow/api.py

@@ -333,7 +333,12 @@ def _to_bibtex(doi, template, idx):
         )
         return doi
 
-    return response.text
+    # doi.org may not honor requested charset, to safeguard force a bytestream with
+    # response.content, then decode into UTF-8.
+    bibtex = response.content.decode()
+
+    # doi.org / crossref may still point to the no longer preferred proxy service
+    return bibtex.replace('http://dx.doi.org/', 'https://doi.org/')
 
 
 def _normalize_ext(value):

templateflow/tests/test_api.py

@@ -1,9 +1,77 @@
 """Test citations."""
+
 import pytest
 
 from .. import api
 
 
+class Bibtex:
+    def __init__(self, bibtex):
+        self.text = bibtex
+        self.url_only = False
+        self.etype = None
+        self.citekey = None
+        self.pairs = {}
+
+        # DOI could not be converted
+        if self.text.startswith("http"):
+            self.url_only = True
+        else:
+            self._parse_bibtex()
+
+    def _parse_bibtex(self):
+        import re
+
+        try:
+            self.etype = re.search(r"@(\w+)", self.text).group(1)
+        except AttributeError:
+            raise TypeError(f"Invalid bibtex: {self.text}")
+        try:
+            self.citekey = re.search(r"@[^{]*{([^,\s]+)", self.text).group(1)
+        except AttributeError:
+            raise TypeError(f"Invalid bibtex: {self.text}")
+        self.pairs = {
+            key: val for key, val in re.findall(r"(\w+)=(\{[^{}]+\})", self.text)
+        }
+
+    def get(self, val):
+        return self.pairs.get(val)
+
+    def __str__(self):
+        return self.text
+
+    def __repr__(self):
+        return f'@{self.etype}{{{self.citekey}, {", ".join([f"{key} = {val}" for key, val in self.pairs.items()])}}}'
+
+    def __eq__(self, other):
+        if isinstance(other, Bibtex):
+            if self.url_only and self.text == other.text:
+                return True
+            if (
+                self.etype == other.etype
+                and self.citekey == other.citekey
+                and self.pairs == other.pairs
+            ):
+                return True
+        return False
+
+    def assert_same(self, other):
+        """Convenience method to find deviations between two Bibtex objects"""
+        assert isinstance(other, Bibtex)
+        assert self.etype == other.etype, "Mismatched entry types"
+        assert self.citekey == other.citekey, "Mismatched citekeys"
+        for key in self.pairs.keys():
+            assert key in other.pairs, f"Key ({key}) missing from other"
+            assert (
+                self.pairs[key] == other.pairs[key]
+            ), f"Key ({key}) mismatched\n\n{self.pairs[key]}\n\n{other.pairs[key]}"
+
+        for key in other.pairs.keys():
+            assert key in self.pairs, f"Key ({key}) missing from pairs"
+
+        assert self.pairs == other.pairs, "Dictionaries do not match"
+
+
 # test setup to avoid cluttering pytest parameterize
 mni2009_urls = [
     "https://doi.org/10.1016/j.neuroimage.2010.07.033",
@@ -14,30 +82,32 @@
 
 mni2009_fbib = """\
 @article{Fonov_2011,
-\tdoi = {10.1016/j.neuroimage.2010.07.033},
-\turl = {https://doi.org/10.1016%2Fj.neuroimage.2010.07.033},
-\tyear = 2011,
-\tmonth = {jan},
-\tpublisher = {Elsevier {BV}},
-\tvolume = {54},
-\tnumber = {1},
-\tpages = {313--327},
-\tauthor = {Vladimir Fonov and Alan C. Evans and Kelly Botteron and C. Robert \
-Almli and Robert C. McKinstry and D. Louis Collins},
-\ttitle = {Unbiased average age-appropriate atlases for pediatric studies},
-\tjournal = {{NeuroImage}}
+DOI={10.1016/j.neuroimage.2010.07.033},
+url={https://doi.org/10.1016/j.neuroimage.2010.07.033},
+year={2011},
+publisher={Elsevier BV},
+ISSN={1053-8119},
+volume={54},
+number={1},
+pages={313–327},
+author={Fonov, Vladimir and Evans, Alan C. and Botteron, Kelly and Almli, C. Robert \
+and McKinstry, Robert C. and Collins, D. Louis},
+title={Unbiased average age-appropriate atlases for pediatric studies},
+journal={NeuroImage}
 }"""
 
 mni2009_lbib = """\
-@incollection{Collins_1999,
-\tdoi = {10.1007/3-540-48714-x_16},
-\turl = {https://doi.org/10.1007%2F3-540-48714-x_16},
-\tyear = 1999,
-\tpublisher = {Springer Berlin Heidelberg},
-\tpages = {210--223},
-\tauthor = {D. Louis Collins and Alex P. Zijdenbos and Wim F. C. Baar{\\'{e}} and Alan C. Evans},
-\ttitle = {{ANIMAL}$\\mathplus${INSECT}: Improved Cortical Structure Segmentation},
-\tbooktitle = {Lecture Notes in Computer Science}
+@inbook{Collins_1999,
+DOI={10.1007/3-540-48714-x_16},
+url={https://doi.org/10.1007/3-540-48714-X_16},
+year={1999},
+publisher={Springer Berlin Heidelberg},
+pages={210–223},
+ISBN={9783540487142},
+ISSN={0302-9743}
+author={Collins, D. Louis and Zijdenbos, Alex P. and Baaré, Wim F. C. and Evans, Alan C.},
+title={ANIMAL+INSECT: Improved Cortical Structure Segmentation},
+booktitle={Information Processing in Medical Imaging}
 }"""
 
 fslr_urls = [
@@ -47,18 +117,18 @@
 
 fslr_fbib = """\
 @article{Van_Essen_2011,
-\tdoi = {10.1093/cercor/bhr291},
-\turl = {https://doi.org/10.1093%2Fcercor%2Fbhr291},
-\tyear = 2011,
-\tmonth = {nov},
-\tpublisher = {Oxford University Press ({OUP})},
-\tvolume = {22},
-\tnumber = {10},
-\tpages = {2241--2262},
-\tauthor = {D. C. Van Essen and M. F. Glasser and D. L. Dierker and J. Harwell and T. Coalson},
-\ttitle = {Parcellations and Hemispheric Asymmetries of Human Cerebral Cortex Analyzed on \
+DOI={10.1093/cercor/bhr291},
+ISSN={1460-2199},
+url={https://doi.org/10.1093/cercor/bhr291},
+year={2011},
+publisher={Oxford University Press (OUP)},
+volume={22},
+number={10},
+pages={2241–2262},
+author={Van Essen, D. C. and Glasser, M. F. and Dierker, D. L. and Harwell, J. and Coalson, T.},
+title={Parcellations and Hemispheric Asymmetries of Human Cerebral Cortex Analyzed on \
 Surface-Based Atlases},
-\tjournal = {Cerebral Cortex}
+journal={Cerebral Cortex}
 }"""
 
 fslr_lbib = (
@@ -67,33 +137,50 @@
 
 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}
+DOI={10.1002/(sici)1097-0193(1999)8:4<272::aid-hbm10>3.0.co;2-4},
+ISSN={1097-0193},
+url={https://doi.org/10.1002/(sici)1097-0193(1999)8:4<272::aid-hbm10>3.0.co;2-4},
+year={1999},
+publisher={Wiley},
+volume={8},
+number={4},
+pages={272–284},
+author={Fischl, Bruce and Sereno, Martin I. and Tootell, Roger B.H. and Dale, Anders M.},
+title={High-resolution intersubject averaging and a coordinate system for the cortical surface},
+journal={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", ["https://doi.org/10.1002/(sici)1097-0193(1999)8:4%3C272::aid-hbm10%3E3.0.co;2-4"], fsaverage_fbib, 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):
     """Check the correct composition of citations."""
     assert api.get_citations(template) == urls
     bibs = api.get_citations(template, bibtex=True)
     if bibs:
-        assert "".join(bibs[0]) == fbib
-        assert len(bibs) == 1 if lbib is None else "".join(bibs[-1]) == lbib
+        bib0 = Bibtex(bibs[0])
+        exp0 = Bibtex(fbib)
+        assert bib0 == exp0
+        if lbib is not None:
+            bib1 = Bibtex(bibs[-1])
+            exp1 = Bibtex(lbib)
+            assert bib1 == exp1
+        else:
+            assert len(bibs) == 1
+
     else:
         # no citations currently
         assert False
@@ -108,7 +195,7 @@ def test_pybids_magic_get():
 
     with pytest.raises(TypeError):
         api.ls_atlases("MNI152NLin6ASym")
-    
+
     # Existing layout.get_* should not be bubbled to the layout
     # (that means, raise an AttributeError instead of a BIDSEntityError)
     with pytest.raises(AttributeError):