Joss fix CI (#38)

.github/workflows/update-requirements.yml

@@ -72,7 +72,7 @@ jobs:
       - name: Install additional dependencies
         run: sudo sh ./install.sh
       - name: Run tests
-        run: pytest --durations=20
+        run: pytest --durations=20 -s src/image2structure -m "not slow"
         env:
           TOKEN_GITHUB: ${{ secrets.TOKEN_GITHUB }}
           PERSPECTIVE_API_KEY: ${{ secrets.PERSPECTIVE_API_KEY }}

README.md

@@ -96,4 +96,6 @@ Then, install the dependencies and git hook scripts:
 
 To run unit tests:
 
-    python -m pytest
+    python -m pytest -s src/image2structure -m "not slow" # Run all tests except ones using OpenArchives
+    python -m pytest -s src/image2structure -m "slow" # Run only tests using OpenArchives
+    python -m pytest -s src/image2structure # Run all tests

pytest.ini

@@ -0,0 +1,3 @@
+[pytest]
+markers =
+    slow: marks tests as slow (deselect with '-m "not slow"')

src/image2structure/fetch/test_arxiv_fetcher.py

@@ -6,6 +6,9 @@
 from image2structure.fetch.arxiv_fetcher import ArxivFetcher
 from image2structure.fetch.fetcher import ScrapeResult, DownloadError
 
+# This test often causes issues in CI dur to 503 error from OpenArchives,
+# so it is disabled by default.
+
 
 class TestArxivFetcher:
     def setup_method(self, method):
@@ -27,14 +30,17 @@ def setup_method(self, method):
     def teardown_method(self, method):
         shutil.rmtree(self.data_path)
 
+    @pytest.mark.slow
     def test_scrape_runs(self):
         results = self.fetcher.scrape(1)
         assert len(results) == 1
 
+    @pytest.mark.slow
     def test_scrape_count(self):
         results = self.fetcher.scrape(18)
         assert len(results) == 18
 
+    @pytest.mark.slow
     def test_download_runs(self):
         results = self.fetcher.scrape(1)
 

src/image2structure/test_collect.py

@@ -1,6 +1,7 @@
 from dotenv import load_dotenv
 
 import os
+import pytest
 import shutil
 
 from image2structure.collect import run, get_args_parser, get_runner_from_args
@@ -42,6 +43,7 @@ def test_webpage(self):
         runner: Runner = get_runner_from_args(args)
         run(runner, args)
 
+    @pytest.mark.slow
     def test_latex(self):
         args = get_args_parser()[0].parse_args(
             [