Merge pull request #82 from shyamd/fix_pandoc

Fix Pandoc

.github/workflows/testing.yml

@@ -21,9 +21,6 @@ jobs:
       with:
         python-version: 3.7
 
-    - name: Install Pandoc
-      run: sudo apt-get install pandoc
-
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -53,7 +50,7 @@ jobs:
       matrix:
         os: [ubuntu-latest]
         python-version: [3.6, 3.7, 3.8]
-
+        pandoc-version: [2.9.2, 2.14.0.3]
     runs-on: ${{ matrix.os }}
 
     steps:
@@ -64,8 +61,9 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install Pandoc
-      run: sudo apt-get install pandoc pandoc-citeproc
+    - uses: r-lib/actions/setup-pandoc@master
+      with:
+        pandoc-version: ${{ matrix.pandoc-version }}
 
     - name: Install Python dependencies
       run: |
@@ -81,7 +79,7 @@ jobs:
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
-        
+
   merge-deps:
     needs:
       - lint

README.md

@@ -40,7 +40,7 @@ The footnotes extension is how citations are linked for now.
 - `bib_command` - The command for your bibliography, defaults to `\bibliography`
 - `full_bib_command` - The command for your bibliography, defaults to `\full_bibliography`
 - `csl_file` - Bibtex CSL file to format the citation with, defaults to None, using a built in plain format instead
-- `unescape_for_arithmatex` - Optional; set to `True` to avoid the `\(` `\)` [issue](https://github.com/shyamd/mkdocs-bibtex/issues/3) with [pymdownx.arithmatex](https://facelessuser.github.io/pymdown-extensions/extensions/arithmatex/) 
+- `unescape_for_arithmatex` - Optional; set to `True` to avoid the `\(` `\)` [issue](https://github.com/shyamd/mkdocs-bibtex/issues/3) with [pymdownx.arithmatex](https://facelessuser.github.io/pymdown-extensions/extensions/arithmatex/)
 
 ## Usage
 

mkdocs_bibtex/plugin.py

@@ -1,6 +1,5 @@
-import glob
-import os.path
 import re
+from pathlib import Path
 import tempfile
 from collections import OrderedDict
 
@@ -30,12 +29,15 @@ class BibTexPlugin(BasePlugin):
     """
 
     config_scheme = [
-        ("bib_file", config_options.Type(str, required=False)),
-        ("bib_dir", config_options.Type(str, required=False)),
-        ("cite_style", config_options.Type(str, default="plain")),
+        ("bib_file", config_options.File(exists=True, required=False)),
+        ("bib_dir", config_options.Dir(exists=True, required=False)),
+        (
+            "cite_style",
+            config_options.Choice(choices=["plain", "pandoc"], default="plain"),
+        ),
         ("bib_command", config_options.Type(str, default="\\bibliography")),
         ("full_bib_command", config_options.Type(str, default="\\full_bibliography")),
-        ("csl_file", config_options.Type(str, required=False)),
+        ("csl_file", config_options.File(exists=True, required=False)),
         ("unescape_for_arithmatex", config_options.Type(bool, required=False)),
     ]
 
@@ -48,25 +50,19 @@ def on_config(self, config):
         """
         Loads bibliography on load of config
         """
-        config_path = os.path.dirname(config.config_file_path)
 
         bibfiles = []
 
         if self.config.get("bib_file", None) is not None:
-            bibfiles.append(get_path(self.config["bib_file"], config_path))
+            bibfiles.append(self.config["bib_file"])
         elif self.config.get("bib_dir", None) is not None:
-            bibfiles.extend(
-                glob.glob(
-                    get_path(os.path.join(self.config["bib_dir"], "*.bib"), config_path)
-                )
-            )
+            bibfiles.extend(Path(self.config["bib_dir"]).glob("*.bib"))
         else:
             raise Exception("Must supply a bibtex file or directory for bibtex files")
 
         # load bibliography data
         refs = {}
         for bibfile in bibfiles:
-            bibfile = get_path(bibfile, config_path)
             bibdata = parse_file(bibfile)
             refs.update(bibdata.entries)
 
@@ -158,7 +154,7 @@ def format_citations(self, citations):
                 entry_text = formatted_entry.text.render(backend)
                 entry_text = entry_text.replace("\n", " ")
                 if self.unescape_for_arithmatex:
-                    entry_text = entry_text.replace('\(', '(').replace('\)', ')')
+                    entry_text = entry_text.replace("\(", "(").replace("\)", ")")
             # Local reference list for this file
             references[key] = entry_text
             # Global reference list for all files
@@ -179,41 +175,49 @@ def full_bibliography(self):
         return "\n".join(full_bibliography)
 
 
-def get_path(path, base_path):
-    if path is None:
-        return None
-    elif os.path.isabs(path):
-        return path
-    else:
-        return os.path.abspath(os.path.join(base_path, path))
-
-
 def to_markdown_pandoc(entry, csl_path):
     """
     Converts the PyBtex entry into formatted markdown citation text
     """
     bibtex_string = BibliographyData(entries={entry.key: entry}).to_string("bibtex")
-    citation_text = """
+    if tuple(int(ver) for ver in pypandoc.get_pandoc_version().split(".")) >= (
+        2,
+        11,
+    ):
+        markdown = pypandoc.convert_text(
+            source=bibtex_string,
+            to="markdown-citations",
+            format="bibtex",
+            extra_args=[
+                "--citeproc",
+                "--csl",
+                csl_path,
+            ],
+        )
+
+        citation_regex = re.compile(
+            r"\{\.csl-left-margin\}\[(.*)\]\{\.csl-right-inline\}"
+        )
+        citation = citation_regex.findall(" ".join(markdown.split("\n")))[0]
+    else:
+        # Older citeproc-filter version of pandoc
+        with tempfile.TemporaryDirectory() as tmpdir:
+            bib_path = Path(tmpdir).joinpath("temp.bib")
+            with open(bib_path, "w") as bibfile:
+                bibfile.write(bibtex_string)
+            citation_text = """
 ---
 nocite: '@*'
 ---
 """
 
-    with tempfile.TemporaryDirectory() as tmpdir:
-        bib_path = os.path.join(tmpdir, "temp.bib")
-        with open(bib_path, "w") as bibfile:
-            bibfile.write(bibtex_string)
-
-        # Call Pandoc.
-        markdown = pypandoc.convert_text(
-            source=citation_text,
-            to="markdown_strict-citations",
-            format="md",
-            extra_args=["--csl", csl_path, "--bibliography", bib_path],
-            filters=["pandoc-citeproc"],
-        )
-
-    # TODO: Perform this extraction better
-    markdown = markdown.split("\n")[0][2:]
+            markdown = pypandoc.convert_text(
+                source=citation_text,
+                to="markdown_strict",
+                format="md",
+                extra_args=["--csl", csl_path, "--bibliography", bib_path],
+                filters=["pandoc-citeproc"],
+            )
 
-    return str(markdown)
+        citation = markdown.replace("\n", " ")[4:]
+    return citation

mkdocs_bibtex/test_plugin.py

@@ -24,13 +24,13 @@ def test_unescape_for_arithmatex(self):
         self.plugin.unescape_for_arithmatex = True
         self.assertIn(
             "First Author and Second Author\. Test Title (TT)\. *Testing Journal (TJ)*, 2019",
-            self.plugin.format_citations(test_data.entries.items())["test"]
+            self.plugin.format_citations(test_data.entries.items())["test"],
         )
 
         self.plugin.unescape_for_arithmatex = False
         self.assertIn(
             "First Author and Second Author\. Test Title \(TT\)\. *Testing Journal \(TJ\)*, 2019",
-            self.plugin.format_citations(test_data.entries.items())["test"]
+            self.plugin.format_citations(test_data.entries.items())["test"],
         )
 
     def test_config_one_bibtex_file(self):
@@ -62,6 +62,20 @@ def test_format_citations(self):
         )
         # TODO: Check CSL
 
+    def test_long_citation(self):
+        test_data = parse_file(os.path.join(test_files_dir, "long_cite.bib"))
+        self.plugin.csl_file = None
+        self.assertIn(
+            "Benjamin L\\. De Bivort and Bruno Van Swinderen",
+            self.plugin.format_citations(test_data.entries.items())["Bivort2016"],
+        )
+
+        self.plugin.csl_file = os.path.join(test_files_dir, "nature.csl")
+        self.assertIn(
+            "De Bivort, B. L. & Van Swinderen",
+            self.plugin.format_citations(test_data.entries.items())["Bivort2016"],
+        )
+
     def test_full_bibliography(self):
         test_data = parse_file(os.path.join(test_files_dir, "single.bib"))
         self.plugin.csl_file = None

test_files/long_cite.bib

@@ -0,0 +1,13 @@
+@article{Bivort2016,
+  title = {Evidence for Selective Attention in the Insect Brain},
+  author = {De Bivort, Benjamin L. and Van Swinderen, Bruno},
+  year = {2016},
+  volume = {15},
+  pages = {1--7},
+  issn = {22145753},
+  doi = {10.1016/j.cois.2016.02.007},
+  abstract = {The capacity for selective attention appears to be required by any animal responding to an environment containing multiple objects, although this has been difficult to study in smaller animals such as insects. Clear operational characteristics of attention however make study of this crucial brain function accessible to any animal model. Whereas earlier approaches have relied on freely behaving paradigms placed in an ecologically relevant context, recent tethered preparations have focused on brain imaging and electrophysiology in virtual reality environments. Insight into brain activity during attention-like behavior has revealed key elements of attention in the insect brain. Surprisingly, a variety of brain structures appear to be involved, suggesting that even in the smallest brains attention might involve widespread coordination of neural activity.},
+  journal = {Current Opinion in Insect Science},
+  keywords = {attention,bees,drosophila,insects},
+  pmid = {27436727}
+}