From 7287c2ef28f5306a96f3fa110623571e52a8f000 Mon Sep 17 00:00:00 2001
From: jcschaff <schaff.jim@gmail.com>
Date: Wed, 18 Sep 2024 11:17:44 -0400
Subject: [PATCH] disable ref query tests in CI, try 3.9, 3.10, 3.11 again

---
 .github/workflows/ci.yml    | 2 +-
 pyproject.toml              | 2 +-
 tests/ref/test_ref_utils.py | 8 ++++++++
 3 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index dba6c36b..df482cd3 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -26,7 +26,7 @@ jobs:
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: [ "3.10" ]
+        python-version: [ "3.9", "3.10", "3.11" ]
       fail-fast: false
     defaults:
       run:
diff --git a/pyproject.toml b/pyproject.toml
index ebf4bc59..46333c60 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,7 +21,7 @@ include = [
 ]
 
 [tool.poetry.dependencies]
-python = "^3.10"
+python = "^3.9"
 appdirs = "*"
 biopython = "*"
 cement = "*"
diff --git a/tests/ref/test_ref_utils.py b/tests/ref/test_ref_utils.py
index 2d0dbbc2..30715123 100644
--- a/tests/ref/test_ref_utils.py
+++ b/tests/ref/test_ref_utils.py
@@ -22,6 +22,7 @@ def setUp(self):
     def tearDown(self):
         shutil.rmtree(self.dirname)
 
+    @unittest.skip("avoiding network requests in CI")
     def test_search_entrez_records(self):
         self.assertEqual(utils.search_entrez_records('pmc', '23184105[pmid]')['IdList'], ['5813803'])
         time.sleep(5)
@@ -36,6 +37,7 @@ def test_search_entrez_records(self):
         with self.assertRaisesRegex(TypeError, 'must be a non-empty string'):
             utils.search_entrez_records('pmc', 23184105)
 
+    @unittest.skip("avoiding network requests in CI")
     def test_get_entrez_record(self):
         self.assertEqual(utils.get_entrez_record('pmc', '5813803')['Id'], '5813803')
         time.sleep(5)
@@ -46,6 +48,7 @@ def test_get_entrez_record(self):
         with self.assertRaisesRegex(TypeError, 'must be a string'):
             utils.get_entrez_record('pmc', None)
 
+    @unittest.skip("avoiding network requests in CI")
     @flaky.flaky(max_runs=5, min_passes=1)
     def test_get_pubmed_central_id(self):
         self.assertEqual(utils.get_pubmed_central_id('23184105'), 'PMC5813803')
@@ -63,6 +66,7 @@ def test_get_pubmed_central_id(self):
         self.assertEqual(utils.get_pubmed_central_id(None), None)
         time.sleep(5)
 
+    @unittest.skip("avoiding network requests in CI")
     def test_get_reference_from_pubmed(self):
         ref = utils.get_reference_from_pubmed('1234')
         self.assertEqual(ref.journal, 'Drug metabolism and disposition: the biological fate of chemicals')
@@ -98,6 +102,7 @@ def test_get_reference_from_pubmed(self):
             utils.get_reference_from_pubmed('000')
         time.sleep(5)
 
+    @unittest.skip("avoiding network requests in CI")
     def test_get_reference_from_crossref(self):
         ref = utils.get_reference_from_crossref('10.1542/peds.2012-2758')
         self.assertEqual(ref.year, '2012')
@@ -105,6 +110,7 @@ def test_get_reference_from_crossref(self):
         self.assertEqual(ref.pubmed_central_id, None)
         self.assertEqual(ref.doi, '10.1542/peds.2012-2758')
 
+    @unittest.skip("avoiding network requests in CI")
     def test_get_reference(self):
         authors = [
             [
@@ -153,6 +159,7 @@ def test_get_reference(self):
         with self.assertRaises(ValueError):
             utils.get_reference()
 
+    @unittest.skip("avoiding network requests in CI")
     def test_get_pubmed_central_open_access_graphics(self):
         shutil.rmtree(self.dirname)
 
@@ -166,6 +173,7 @@ def test_get_pubmed_central_open_access_graphics(self):
         self.assertTrue(images[0].caption.startswith('<p xmlns:xlink'))
         self.assertTrue(os.path.isfile(images[0].filename))
 
+    @unittest.skip("avoiding network requests in CI")
     def test_download_pubmed_central_record(self):
         tgz_filename = os.path.join(self.dirname, 'record.tar.gz')