v0.10.2: fix pandoc error based on separate BibTeX file

CHANGELOG.md

@@ -15,6 +15,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0).
 
 ### Fixed
 
+## 0.10.2 - 2023-10-15
+
+### Fixed
+
+- paper_md: export BibTeX file and replace keys containing `.` to prevent pandoc error
+
 ## 0.10.1 - 2023-10-06
 
 ### Changed

CITATION.cff

@@ -8,6 +8,6 @@ authors:
   given-names: "Julian"
   orcid: "https://orcid.org/0000-0003-2682-8036"
 title: "CoLRev: An open-source environment for collaborative reviews"
-version: 0.10.1
-date-released: 2023-10-06
+version: 0.10.2
+date-released: 2023-10-15
 url: "https://github.com/CoLRev-Environment/colrev"

colrev/dataset.py

@@ -60,6 +60,7 @@ class Dataset:
         "data/prep_man/records_prep_man.bib",
         "data/prep/",
         "data/dedupe/",
+        "data/data/sample_references.bib",
     ]
     DEPRECATED_GIT_IGNORE_ITEMS = [
         "missing_pdf_files.csv",

colrev/ops/built_in/data/paper_md.py

@@ -29,6 +29,7 @@
     import colrev.ops.data
 
 
+# pylint: disable=too-many-instance-attributes
 @zope.interface.implementer(colrev.env.package_manager.DataPackageEndpointInterface)
 @dataclass
 class PaperMarkdown(JsonSchemaMixin):
@@ -53,6 +54,7 @@ class PaperMarkdown(JsonSchemaMixin):
     the corresponding record will be marked as rev_synthesized."""
 
     NON_SAMPLE_REFERENCES_RELATIVE = Path("non_sample_references.bib")
+    SAMPLE_REFERENCES_RELATIVE = Path("sample_references.bib")
 
     ci_supported: bool = False
 
@@ -109,6 +111,9 @@ def __init__(
         self.non_sample_references = (
             data_operation.review_manager.data_dir / self.NON_SAMPLE_REFERENCES_RELATIVE
         )
+        self.sample_references = (
+            data_operation.review_manager.data_dir / self.SAMPLE_REFERENCES_RELATIVE
+        )
         self.data_operation = data_operation
 
         self.settings.paper_output = (
@@ -128,6 +133,8 @@ def __init__(
         )
         self.__temp_path.mkdir(exist_ok=True, parents=True)
 
+        self.review_manager = data_operation.review_manager
+
     # pylint: disable=unused-argument
     @classmethod
     def add_endpoint(cls, operation: colrev.ops.data.Data, params: str) -> None:
@@ -651,6 +658,15 @@ def __create_non_sample_references_bib(self) -> None:
             except AttributeError:
                 pass
 
+    def __copy_references_bib(self) -> None:
+        records = self.review_manager.dataset.load_records_dict()
+        for record_id, record_dict in records.items():
+            record_dict = {k.replace(".", "_"): v for k, v in record_dict.items()}
+            records[record_id] = record_dict
+        self.review_manager.dataset.save_records_dict_to_file(
+            records=records, save_path=self.sample_references
+        )
+
     def __call_docker_build_process(
         self, *, data_operation: colrev.ops.data.Data, script: str
     ) -> None:
@@ -700,6 +716,7 @@ def build_paper(self, *, data_operation: colrev.ops.data.Data) -> None:
 
         self.__retrieve_default_csl()
         self.__create_non_sample_references_bib()
+        self.__copy_references_bib()
 
         word_template = self.settings.word_template
 

colrev/ops/upgrade.py

@@ -149,6 +149,12 @@ def main(self) -> None:
                 "script": self.__migrate_0_10_1,
                 "released": True,
             },
+            {
+                "version": CoLRevVersion("0.10.1"),
+                "target_version": CoLRevVersion("0.10.2"),
+                "script": self.__migrate_0_10_2,
+                "released": True,
+            },
         ]
         print(f"installed_colrev_version: {installed_colrev_version}")
         print(f"settings_version: {settings_version}")
@@ -523,8 +529,18 @@ def __migrate_0_10_1(self) -> bool:
                 source["search_type"] = "FILES"
 
         self.__save_settings(settings)
+        return self.repo.is_dirty()
 
-        return False
+    def __migrate_0_10_2(self) -> bool:
+        paper_md_path = Path("data/data/paper.md")
+        paper_md_content = paper_md_path.read_text(encoding="utf-8")
+        paper_md_content = paper_md_content.replace(
+            "data/records.bib", "data/data/sample_references.bib"
+        )
+        paper_md_path.write_text(paper_md_content, encoding="utf-8")
+        self.repo.index.add([str(paper_md_path)])
+
+        return self.repo.is_dirty()
 
 
 # Note: we can ask users to make decisions (when defaults are not clear)

colrev/template/paper_md/paper.md

@@ -1,7 +1,7 @@
 ---
 title: "{{project_title}}"
 author: "{{author}}"
-bibliography: [data/records.bib,data/data/non_sample_references.bib]
+bibliography: [data/data/sample_references.bib,data/data/non_sample_references.bib]
 figPrefix: "Figure"
 tblPrefix: "Table"
 csl: "https://raw.githubusercontent.com/citation-style-language/styles/master/apa.csl"

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "colrev"
-version = "0.10.1"
+version = "0.10.2"
 description = "CoLRev: An open-source environment for collaborative reviews"
 authors = ["Gerit Wagner <gerit.wagner@uni-bamberg.de>", "Julian Prester <julian.prester@sydney.edu.au>"]
 license = "MIT"

release-checklist.md

@@ -8,9 +8,9 @@
 - Run `colrev env --update_package_list`.
 - Update Docker image versions and test.
 - Collect release notes and update the `CHANGELOG.md`.
-- Update version and date in `CITATION.cff`.
+- Update **version** and **date**  and date in `CITATION.cff`.
 - Update version in `SECURITY.md`.
-- Update the **version** and **date** in `pyproject.toml`. Check whether other parts of the `pyproject.toml` need to be updated. Check whether dependencies can be removed.
+- Update the version in `pyproject.toml`. Check whether other parts of the `pyproject.toml` need to be updated. Check whether dependencies can be removed.
 - Update the Github milestones, close current one, make plans for the next milestones
 - Commit the changes (`release 0.10.0`).
 - Push to Github. Check whether the installation, tests, and pre-commit hooks pass.

tests/2_ops/check_test.py

@@ -14,7 +14,7 @@ def test_checks(  # type: ignore
 
     checker = colrev.checker.Checker(review_manager=base_repo_review_manager)
 
-    expected = ["0.10.1", "0.10.1"]
+    expected = ["0.10.2", "0.10.2"]
     actual = checker.get_colrev_versions()
     assert expected == actual