tests: Add data with multiple dois for tests and update pyproject.toml (#16)

Author: xmnlab

.github/workflows/main.yaml

@@ -29,9 +29,9 @@ jobs:
   tests:
     needs: check-branch
     strategy:
+      fail-fast: false
       matrix:
         python_version:
-          - "3.8.1"
           - "3.9"
           - "3.10"
           - "3.11"
@@ -63,6 +63,7 @@ jobs:
           activate-environment: pymedx
           auto-update-conda: true
           conda-solver: libmamba
+          python-version: "${{ matrix.python_version }}"
 
       - name: Install dependencies
         run: |
@@ -97,6 +98,7 @@ jobs:
           activate-environment: pymedx
           auto-update-conda: true
           conda-solver: libmamba
+          python-version: "3.12"
 
       - name: Install dependencies
         run: |

.github/workflows/release.yaml

@@ -33,6 +33,7 @@ jobs:
           activate-environment: pymedx
           auto-update-conda: true
           conda-solver: libmamba
+          python-version: "3.12"
 
       - name: Install deps
         run: poetry install

conda/dev.yaml

@@ -3,10 +3,12 @@ channels:
   - nodefaults
   - conda-forge
 dependencies:
-  - python >=3.8.1,<4
+  - compilers
+  - python
   - pip
-  - poetry
+  - poetry >=2
   - nodejs # used by semantic-release
   - shellcheck
   - pip:
       - paginate
+      - levenshtein==0.25.1 # pep517

poetry.lock

@@ -1,30 +1,39 @@
-[tool.poetry]
+[project]
 name = "pymedx"
 version = "0.5.0"  # semantic-release
 description = "PyMedX is a tool set for handling multimedia files."
 readme = "docs/index.md"
-authors = ["Gijs Wobben <[email protected]>", "Ivan Ogasawara <[email protected]>"]
+authors = [
+  { name = "Gijs Wobben", email = "[email protected]" },
+  { name = "Ivan Ogasawara", email = "[email protected]" },
+  { name = "Ever Vino", email = "[email protected]" },
+]
 packages = [
-  {include = "pymedx", from="src"},
+  {include = "pymedx", from = "src"},
 ]
 license = "MIT"
 exclude = [
   ".git/*",
   ".env*",
 ]
+requires-python = ">3.9,<4"
+dependencies = [
+  "requests (>=2.20.0)",
+  "lxml (>=5.1.0)",
+]
 
-
-[tool.poetry.dependencies]
-python = ">3.8.1,<4"
-requests = ">=2.20.0"
-lxml = "^5.1.0"
+[build-system]
+requires = ["poetry-core>=2", "poetry>=2"]
+build-backend = "poetry.core.masonry.api"
 
 [tool.poetry.group.dev.dependencies]
+python = ">3.9,<4"
+python-dotenv = ">=1.0"
 pytest = ">=7.3.2"
 pytest-cov = ">=4.1.0"
 coverage = ">=7.2.7"
 pre-commit = ">=3.3.2"
-ruff = ">=0.1.5"
+ruff = ">=0.9.5"
 mypy = ">=1.6.0"
 bandit = ">=1.7.5"
 vulture = ">=2.9.1"

pyproject.toml

@@ -1,5 +1,6 @@
 # mypy: disable-error-code="attr-defined"
 """PyMedX package."""
+
 from importlib import metadata as importlib_metadata
 
 from .api import PubMed, PubMedCentral

src/pymedx/__init__.py

@@ -1,4 +1,5 @@
 """API module for PubMed."""
+
 from __future__ import annotations
 
 import datetime

src/pymedx/api.py

@@ -1,4 +1,5 @@
 """Module for handling articles."""
+
 import datetime
 import json
 
@@ -13,18 +14,18 @@ class PubMedArticle:
     """Data class that contains a PubMed article."""
 
     __slots__ = (
-        "pubmed_id",
-        "title",
         "abstract",
-        "keywords",
-        "journal",
-        "publication_date",
         "authors",
-        "methods",
         "conclusions",
-        "results",
         "copyrights",
         "doi",
+        "journal",
+        "keywords",
+        "methods",
+        "publication_date",
+        "pubmed_id",
+        "results",
+        "title",
         "xml",
     )
 
@@ -197,12 +198,12 @@ class PubMedCentralArticle:
 
     # slots which have been implemented
     __slots__ = (
-        "pmc_id",
-        "title",
         "abstract",
-        "publication_date",
         "authors",
         "doi",
+        "pmc_id",
+        "publication_date",
+        "title",
     )
 
     def __init__(

src/pymedx/article.py

@@ -1,4 +1,5 @@
 """Module for functions about book article."""
+
 import datetime
 import json
 
@@ -13,19 +14,19 @@ class PubMedBookArticle:
     """Data class that contains a PubMed article."""
 
     __slots__ = (
-        "pubmed_id",
-        "title",
         "abstract",
-        "publication_date",
         "authors",
         "copyrights",
         "doi",
         "isbn",
         "language",
+        "publication_date",
         "publication_type",
-        "sections",
         "publisher",
         "publisher_location",
+        "pubmed_id",
+        "sections",
+        "title",
     )
 
     def __init__(

src/pymedx/book.py

@@ -1,4 +1,5 @@
 """Module for helper functions."""
+
 from __future__ import annotations
 
 import datetime
@@ -127,8 +128,7 @@ def get_range_months(
         current_end_date = next_month - datetime.timedelta(days=next_month.day)
 
         # Adjust the end date if it goes beyond the specified end_date
-        if current_end_date > end_date:
-            current_end_date = end_date
+        current_end_date = min(current_end_date, end_date)
 
         date_ranges.append((current_start_date, current_end_date))
 

src/pymedx/helpers.py

@@ -0,0 +1,2 @@
+NCBI_API_KEY=${NCBI_API_KEY}
+SERVICE_EMAIL=${SERVICE_EMAIL}

tests/.env.tpl

@@ -1,9 +1,14 @@
 """Configuration for the tests."""
+
 import os
 
+from pathlib import Path
+from typing import Dict, cast
+
 import pytest
 import requests_cache
 
+from dotenv import dotenv_values, load_dotenv
 from pymedx.api import PubMed, PubMedCentral
 
 
@@ -28,8 +33,18 @@ def setup_request_cache():
     # requests_cache doesn't require special teardown
 
 
+@pytest.fixture(scope="session")
+def env() -> dict[str, str]:
+    """Return a fixture for the environment variables from .env."""
+    dotenv_file = Path(__file__).parent / ".env"
+    if dotenv_file.exists():
+        load_dotenv(dotenv_file)
+        return cast(Dict[str, str], dotenv_values(dotenv_file) or {})
+    return {}
+
+
 @pytest.fixture(scope="session", autouse=True)
-def pubmed() -> PubMed:
+def pubmed(env) -> PubMed:
     """Fixture to create a PubMed instance."""
     params = dict(tool="TestTool", email="[email protected]")
 
@@ -41,7 +56,7 @@ def pubmed() -> PubMed:
 
 
 @pytest.fixture(scope="session", autouse=True)
-def pmc() -> PubMedCentral:
+def pmc(env) -> PubMedCentral:
     """Fixture to create a PubMed instance."""
     params = dict(tool="TestTool", email="[email protected]")
 

tests/conftest.py

@@ -1,6 +1,5 @@
 """Tests for the api module."""
 
-
 from pymedx.api import (
     PubMed,
 )

tests/data/pmid_ 31815395.xml

@@ -1,4 +1,5 @@
 """Test for the article module."""
+
 import datetime
 
 import pytest

tests/test_api.py

@@ -1,4 +1,5 @@
 """Tests for the book module."""
+
 import datetime
 
 import pytest

tests/test_article.py

@@ -25,9 +25,9 @@ def test_batches(self):
         generated_batches = list(batches(input_list, batch_size))
 
         # Verify
-        assert (
-            generated_batches == expected_batches
-        ), "Batches not generated as expected."
+        assert generated_batches == expected_batches, (
+            "Batches not generated as expected."
+        )
 
     def test_get_content(self):
         """Test the getContent function."""

tests/test_book.py

@@ -1,6 +1,5 @@
 """Tests for the api module."""
 
-
 from pymedx.api import PubMedCentral
 
 

tests/test_helpers.py

@@ -1,4 +1,5 @@
 """Test for the article module."""
+
 import datetime
 
 import pytest