Bump min Papis version

.github/workflows/main.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
       fail-fast: False
 
     steps:

Makefile

@@ -25,10 +25,10 @@ mypy:								## Run (strict) mypy checks
 .PHONY: mypy
 
 pytest:								## Run pytest test and doctests
-	python -m pytest -rswx --cov=papis_zotero -v -s tests
+	python -m pytest -rswx -v -s tests
 .PHONY: pytest
 
 ci-install:							## Run pip and install dependencies on CI
-	python -m pip install --upgrade pip setuptools wheel
+	python -m pip install --upgrade pip hatchling wheel
 	python -m pip install -e '.[develop]'
 .PHONY: ci-install

papis_zotero/__init__.py

@@ -12,13 +12,13 @@
 logger = papis.logging.get_logger(__name__)
 
 
-@click.group("zotero")                  # type: ignore[arg-type]
+@click.group("zotero")
 @click.help_option("-h", "--help")
 def main() -> None:
     """Zotero interface for papis."""
 
 
-@main.command("serve")                  # type: ignore[arg-type]
+@main.command("serve")
 @click.help_option("-h", "--help")
 @click.option("--port",
               help="Port to listen to",
@@ -56,7 +56,7 @@ def serve(address: str, port: int, set_list: List[Tuple[str, str]],) -> None:
     httpd.serve_forever()
 
 
-@main.command("import")                 # type: ignore[arg-type]
+@main.command("import")
 @click.help_option("-h", "--help")
 @click.option(
     "-f",

papis_zotero/bibtex.py

@@ -1,5 +1,6 @@
 import os
-from typing import Optional
+import re
+from typing import Any, Dict, Optional
 
 import papis.bibtex
 import papis.commands.add
@@ -8,6 +9,8 @@
 
 logger = papis.logging.get_logger(__name__)
 
+RE_SEPARATOR = re.compile(r"\s*,\s*")
+
 
 def add_from_bibtex(bib_file: str,
                     out_folder: Optional[str] = None,
@@ -18,28 +21,25 @@ def add_from_bibtex(bib_file: str,
     entries = papis.bibtex.bibtex_to_dict(bib_file)
     nentries = len(entries)
     for i, entry in enumerate(entries):
-        # cleanup tags
-        if "date" in entry:
-            date = str(entry.pop("date")).split("-")
-            entry["year"] = int(date[0])    # type: ignore[assignment]
-            entry["month"] = int(date[1])   # type: ignore[assignment]
+        result: Dict[str, Any] = entry.copy()
 
-        if "keywords" in entry:
-            entry["tags"] = entry.pop("keywords")
+        # cleanup date
+        if "date" in result:
+            date = str(result.pop("date")).split("-")
+            result["year"] = int(date[0])
+            result["month"] = int(date[1])
 
-        if "author" not in entry:
-            if "tags" in entry:
-                entry["tags"] = "{} unknown-author".format(entry["tags"])
-            else:
-                entry["tags"] = "unknown-author"
+        # cleanup tags
+        if "keywords" in result:
+            result["tags"] = RE_SEPARATOR.split(result.pop("keywords"))
 
-        if "ref" in entry:
-            entry["ref"] = papis.bibtex.ref_cleanup(entry["ref"])
+        if "ref" in result:
+            result["ref"] = papis.bibtex.ref_cleanup(result["ref"])
         else:
-            entry["ref"] = papis.bibtex.create_reference(entry)
+            result["ref"] = papis.bibtex.create_reference(result)
 
         # get file
-        pdf_file = entry.pop("file", None)
+        pdf_file = result.pop("file", None)
         if pdf_file is not None:
             pdf_file = pdf_file.split(":")[1]
             pdf_file = os.path.join(*pdf_file.split("/"))
@@ -53,8 +53,8 @@ def add_from_bibtex(bib_file: str,
 
         # add to library
         logger.info("[%4d/%-4d] Exporting item with ref '%s'.",
-                    i, nentries, entry["ref"])
+                    i, nentries, result["ref"])
 
         papis.commands.add.run([pdf_file] if pdf_file is not None else [],
-                               data=entry,
+                               data=result,
                                link=link)

papis_zotero/server.py

@@ -33,7 +33,7 @@
         }]),
     _k("tags", [{
         "key": "tags",
-        "action": lambda t: "; ".join(tag["tag"] for tag in t)
+        "action": lambda t: [tag["tag"] for tag in t]
         }]),
     _k("date", [
         {"key": "year", "action": lambda d: int(d.split("-")[0])},

papis_zotero/sql.py

@@ -15,10 +15,6 @@
 
 logger = papis.logging.get_logger(__name__)
 
-# separator between multiple tags
-# FIXME: this should be handled by papis
-ZOTERO_TAG_DELIMITER = " "
-
 # fuzzy date matching
 ISO_DATE_RE = re.compile(r"(?P<year>\d{4})-?(?P<month>\d{2})?-?(?P<day>\d{2})?")
 
@@ -162,11 +158,11 @@ def get_files(connection: sqlite3.Connection, item_id: str, item_key: str,
 """
 
 
-def get_tags(connection: sqlite3.Connection, item_id: str) -> Dict[str, str]:
+def get_tags(connection: sqlite3.Connection, item_id: str) -> Dict[str, List[str]]:
     cursor = connection.cursor()
     cursor.execute(ZOTERO_QUERY_ITEM_TAGS, (item_id,))
 
-    tags = ZOTERO_TAG_DELIMITER.join(str(row[0]) for row in cursor)
+    tags = [str(row[0]) for row in cursor]
     return {"tags": tags} if tags else {}
 
 
@@ -221,7 +217,8 @@ def get_collections(connection: sqlite3.Connection,
 """.format(",".join(["?"] * len(papis_zotero.utils.ZOTERO_EXCLUDED_ITEM_TYPES)))
 
 
-def add_from_sql(input_path: str, out_folder: Optional[str] = None,
+def add_from_sql(input_path: str,
+                 out_folder: Optional[str] = None,
                  link: bool = False) -> None:
     """
     :param inpath: path to zotero SQLite database "zoter.sqlite" and
@@ -259,6 +256,7 @@ def add_from_sql(input_path: str, out_folder: Optional[str] = None,
     if out_folder is not None:
         papis.config.set_lib_from_name(out_folder)
 
+    folder_name = papis.config.getstring("add-folder-name")
     for i, (item_id, item_type, item_key, date_added) in enumerate(cursor, start=1):
         # convert fields
         date_added = (
@@ -284,7 +282,7 @@ def add_from_sql(input_path: str, out_folder: Optional[str] = None,
                     i, items_count, item_key, out_folder)
 
         papis.commands.add.run(paths=files, data=item, link=link,
-                               folder_name=papis.config.getstring("add-folder-name")
+                               folder_name=folder_name
                                )
 
     logger.info("Finished exporting from '%s'.", input_path)

pyproject.toml

@@ -1,18 +1,20 @@
 [build-system]
 build-backend = "hatchling.build"
-requires = ["hatchling>=1.10.0"]
+requires = [ "hatchling>=1.10" ]
 
 [project]
 name = "papis-zotero"
-description = "Interact with Zotero using papis"
 version = "0.1.2"
-authors = [{ name = "Alejandro Gallo", email = "aamsgallo@gmail.com" }]
-maintainers = [{ name = "Alejandro Gallo", email = "aamsgallo@gmail.com" }]
+description = "Interact with Zotero using papis"
 readme = "README.rst"
-license = { text = "GPLv3" }
+keywords = [ "bibtex", "biliography", "cli", "management", "papis", "zotero" ]
+license = { text = "GPL-3.0-or-later" }
+maintainers = [ { name = "Alejandro Gallo", email = "aamsgallo@gmail.com" } ]
+authors = [ { name = "Alejandro Gallo", email = "aamsgallo@gmail.com" } ]
+requires-python = ">=3.8"
 classifiers = [
-    "Environment :: Console :: Curses",
     "Environment :: Console",
+    "Environment :: Console :: Curses",
     "Intended Audience :: Developers",
     "Intended Audience :: Education",
     "Intended Audience :: Science/Research",
@@ -29,43 +31,47 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Topic :: Utilities",
 ]
-keywords = ["bibtex", "biliography", "cli", "management", "papis", "zotero"]
-dependencies = ["papis==0.13"]
-
-[project.urls]
-Repository = "https://github.com/papis/papis-zotero"
+dependencies = [ "papis>=0.14,<0.15" ]
 
 [project.optional-dependencies]
-"develop" = [
+develop = [
     "flake8",
     "flake8-bugbear",
+    "flake8-pyproject",
     "flake8-quotes",
-    "Flake8-pyproject",
     "mypy>=0.7",
     "pep8-naming",
     "pytest",
     "pytest-cov",
     "python-coveralls",
-    "types-PyYAML",
-    "types-tqdm",
+    "types-pyyaml",
 ]
 
+[project.urls]
+Repository = "https://github.com/papis/papis-zotero"
+
 [project.entry-points."papis.command"]
-"zotero" = "papis_zotero:main"
+zotero = "papis_zotero:main"
 
 [tool.flake8]
-select = ["B", "D", "E", "F", "N", "Q", "W"]
-extend-ignore = ["B019", "E123", "N818", "W503"]
+select = [ "B", "D", "E", "F", "N", "Q", "W" ]
+extend-ignore = [ "B019", "E123", "N818", "W503" ]
 max-line-length = 88
 inline-quotes = "double"
 multiline-quotes = "double"
 
 [tool.pytest.ini_options]
+addopts = [
+    "--doctest-modules",
+    "--cov=papis_zotero",
+]
 norecursedirs = ".git doc build dist"
 python_files = "*.py"
-markers = ["config_setup: setup for tmp_config",
+markers = [
+    "config_setup: setup for tmp_config",
     "library_setup: setup for tmp_library",
 ]
 
@@ -74,4 +80,4 @@ strict = true
 show_column_numbers = true
 hide_error_codes = false
 pretty = true
-warn_unused_ignores = false
+warn_unused_ignores = true

tests/resources/bibtex/zotero-library.bib

@@ -12,7 +12,7 @@ @article{schaeffer_efficient_2013
 	author = {Schaeffer, Nathanaël},
 	urldate = {2023-02-26},
 	date = {2013-03},
-	langid = {english},
+	langid = {english}
 	file = {Full Text:files/8/Schaeffer - 2013 - Efficient spherical harmonic transforms aimed at p.pdf:application/pdf},
 }
 

tests/resources/bibtex_out.yaml

@@ -12,8 +12,9 @@ journaltitle: Journal of Computational Physics
 langid: english
 month: 7
 pages: 17--38
-ref: ReviewOfSummaSvard2014
-tags: sbp
+ref: svard_review_2014
+tags:
+- sbp
 title: Review of summation-by-parts schemes for initial–boundary-value problems
 type: article
 url: https://linkinghub.elsevier.com/retrieve/pii/S002199911400151X

tests/test_bibtex.py

@@ -7,8 +7,7 @@
 import papis.database
 import papis.document
 import papis_zotero.bibtex
-
-from .testlib import TemporaryLibrary
+from papis.testing import TemporaryLibrary
 
 
 @pytest.mark.skipif(os.name == "nt", reason="encoding is incorrect on windows")

tests/test_sql.py

@@ -6,8 +6,7 @@
 import papis.yaml
 import papis.document
 import papis_zotero.sql
-
-from .testlib import TemporaryLibrary
+from papis.testing import TemporaryLibrary
 
 
 @pytest.mark.skipif(os.name == "nt", reason="encoding is incorrect on windows")