fix: update fMRIPrep version in bibliography at run time

nipreps · Mar 7, 2022 · 13d16af · 13d16af
1 parent e476163
commit 13d16af
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Showing 3 changed files with 9 additions and 7 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -102,7 +102,6 @@ jobs:
               echo "them to your fork with ``git push origin --tags``"
             fi
             sed -i -E "s/(__version__ = )'[A-Za-z0-9.-]+'/\1'${CIRCLE_TAG:-$THISVERSION}'/" wrapper/fmriprep_docker.py
-            sed -i "s/title = {FMRIPrep}/title = {FMRIPrep ${CIRCLE_TAG:-$THISVERSION}}/" fmriprep/data/boilerplate.bib
             # Build docker image
             e=1 && for i in {1..5}; do
               docker build --rm \

diff --git a/fmriprep/cli/workflow.py b/fmriprep/cli/workflow.py
@@ -179,16 +179,21 @@ def build_boilerplate(config_file, workflow):
     citation_files["md"].write_text(boilerplate)
 
     if not config.execution.md_only_boilerplate and citation_files["md"].exists():
+        from pathlib import Path
         from subprocess import check_call, CalledProcessError, TimeoutExpired
         from pkg_resources import resource_filename as pkgrf
-        from shutil import copyfile
+
+        bib_text = Path(pkgrf("fmriprep", "data/boilerplate.bib")).read_text()
+        citation_files["bib"].write_text(
+            bib_text.replace("fMRIPrep <version>", f"fMRIPrep {config.environment.version}")
+        )
 
         # Generate HTML file resolving citations
         cmd = [
             "pandoc",
             "-s",
             "--bibliography",
-            pkgrf("fmriprep", "data/boilerplate.bib"),
+            str(citation_files["bib"]),
             "--citeproc",
             "--metadata",
             'pagetitle="fMRIPrep citation boilerplate"',
@@ -212,7 +217,7 @@ def build_boilerplate(config_file, workflow):
             "pandoc",
             "-s",
             "--bibliography",
-            pkgrf("fmriprep", "data/boilerplate.bib"),
+            str(citation_files["bib"]),
             "--natbib",
             str(citation_files["md"]),
             "-o",
@@ -227,5 +232,3 @@ def build_boilerplate(config_file, workflow):
             config.loggers.cli.warning(
                 "Could not generate CITATION.tex file:\n%s", " ".join(cmd)
             )
-        else:
-            copyfile(pkgrf("fmriprep", "data/boilerplate.bib"), citation_files["bib"])
diff --git a/fmriprep/data/boilerplate.bib b/fmriprep/data/boilerplate.bib
@@ -8,7 +8,7 @@ @article{fmriprep1
 
 @article{fmriprep2,
     author = {Esteban, Oscar and Blair, Ross and Markiewicz, Christopher J. and Berleant, Shoshana L. and Moodie, Craig and Ma, Feilong and Isik, Ayse Ilkay and Erramuzpe, Asier and Kent, James D. andGoncalves, Mathias and DuPre, Elizabeth and Sitek, Kevin R. and Gomez, Daniel E. P. and Lurie, Daniel J. and Ye, Zhifang and Poldrack, Russell A. and Gorgolewski, Krzysztof J.},
-    title = {fMRIPrep},
+    title = {fMRIPrep <version>},
     year = 2018,
     doi = {10.5281/zenodo.852659},
     publisher = {Zenodo},