refactor: use virtual env in server runtime

- include in .env PATH and make docker-compose.yml target depend on .env
- replace deprecated usage of self.assertEquals
https://docs.python.org/3/whatsnew/3.12.html#id3

Makefile

@@ -82,7 +82,7 @@ release-version: .env
 	$(ENVREPLACE) TEST_BASIC_AUTH_PASSWORD $$(openssl rand -base64 42) .env
 
 .PHONY: docker-compose.yml
-docker-compose.yml: base.yml dev.yml staging.yml prod.yml config.mk $(PGPASS_PATH) release-version
+docker-compose.yml: base.yml dev.yml staging.yml prod.yml config.mk $(PGPASS_PATH) release-version .env
 	case "$(DEPLOY_ENVIRONMENT)" in \
 	  dev|staging) docker compose -f base.yml -f $(DEPLOY_ENVIRONMENT).yml config > docker-compose.yml;; \
 	  prod) docker compose -f base.yml -f staging.yml -f $(DEPLOY_ENVIRONMENT).yml config > docker-compose.yml;; \
@@ -100,7 +100,7 @@ secrets: $(SECRETS_DIR) $(GENERATED_SECRETS)
 	done
 
 .PHONY: deploy
-deploy: build .env
+deploy: build
 	docker compose pull db redis elasticsearch
 ifneq ($(DEPLOY_ENVIRONMENT),dev)
 	docker compose pull nginx

deploy/conf/.env.template

@@ -1,8 +1,9 @@
 # Docker build
 # UBUNTU_MIRROR=mirror.arizona.edu
+VIRTUAL_ENV=/home/comses/virtualenvs/comses.venv
 UBUNTU_MIRROR=archive.ubuntu.com
 # set PATH defaults for cron execution
-PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+PATH="${VIRTUAL_ENV}/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
 
 # app settings
 RELEASE_VERSION=
@@ -21,7 +22,7 @@ DISCOURSE_BASE_URL=
 DISCOURSE_API_USERNAME=
 
 # elastic search
-ES_VERSION=7.17.22
+ES_VERSION=7.17.26
 
 # email
 EMAIL_SUBJECT_PREFIX="[CoMSES Net]"

django/core/tests/test_views.py

@@ -197,7 +197,7 @@ def test_mark_spam(self):
         )
         event.refresh_from_db()
         # non-moderators cannot mark content as spam
-        self.assertEquals(response.status_code, 403)
+        self.assertEqual(response.status_code, 403)
         self.assertFalse(event.is_marked_spam)
         # check moderator
         self.client.login(

django/home/tests/test_metrics.py

@@ -39,18 +39,18 @@ def test_convert_timeseries(self):
         )
         for chart_data in highcharts_timeseries:
             # 2012 and 2013 should also be 0
-            self.assertEquals(
+            self.assertEqual(
                 tuple(chart_data["data"][0:2]),
                 (0, 0),
                 "2012-13 should be zeroed out",
             )
             # missing year 2016
-            self.assertEquals(
+            self.assertEqual(
                 chart_data["data"][4],
                 0,
                 f"5th entry (2016) should be 0 {chart_data['name']}",
             )
             self.assertTrue(
                 chart_data["name"] in OS_NAMES, f"Invalid OS name {chart_data['name']}"
             )
-            self.assertEquals(len(chart_data["data"]), 7, "Should be 7 years of data")
+            self.assertEqual(len(chart_data["data"]), 7, "Should be 7 years of data")

django/library/tests/test_datacite_api.py

@@ -50,7 +50,7 @@ def test_mint_new_doi_for_release(self):
         self.assertTrue(self.api.is_datacite_available())
         release = self.codebase.releases.first()
         log, ok = self.api.mint_public_doi(release)
-        self.assertEquals(log.http_status, 200, "should have successfully minted a DOI")
+        self.assertEqual(log.http_status, 200, "should have successfully minted a DOI")
         self.assertTrue(self.api.doi_matches_pattern(doi))
 
     def test_update_metadata_for_release(self):

django/library/tests/test_fs.py

@@ -43,8 +43,8 @@ def test_zipfile_saving(self):
             fs_api=fs_api,
         )
         logs, level = msgs.serialize()
-        self.assertEquals(level, MessageLevels.warning)
-        self.assertEquals(len(logs), 2)
+        self.assertEqual(level, MessageLevels.warning)
+        self.assertEqual(len(logs), 2)
         self.assertEqual(
             set(
                 fs_api.list(StagingDirectories.originals, FileCategoryDirectories.code)
@@ -77,8 +77,8 @@ def test_invalid_zipfile_saving(self):
                 FileCategoryDirectories.code, content=f, name="invalid.zip"
             )
         logs, level = msgs.serialize()
-        self.assertEquals(level, MessageLevels.error)
-        self.assertEquals(len(logs), 1)
+        self.assertEqual(level, MessageLevels.error)
+        self.assertEqual(len(logs), 1)
 
     @classmethod
     def tearDownClass(cls):

django/library/tests/test_models.py

@@ -30,11 +30,11 @@ def setUp(self):
         )
 
     def test_base_dir(self):
-        self.assertEquals(
+        self.assertEqual(
             self.c1.base_library_dir,
             pathlib.Path(settings.LIBRARY_ROOT, str(self.c1.uuid)),
         )
-        self.assertEquals(
+        self.assertEqual(
             self.c1.base_git_dir,
             pathlib.Path(settings.REPOSITORY_ROOT, str(self.c1.uuid)),
         )
@@ -43,8 +43,8 @@ def test_create_release(self):
         release = ReleaseSetup.setUpPublishableDraftRelease(self.c1)
         release.validate_publishable()
         release.publish()
-        self.assertEquals(self.c1.latest_version, release)
-        self.assertEquals(
+        self.assertEqual(self.c1.latest_version, release)
+        self.assertEqual(
             CodebaseRelease.objects.get(
                 codebase=self.c1, version_number=release.version_number
             ),

django/requirements.txt

@@ -30,6 +30,7 @@ elasticsearch>=7.0.0,<8.0.0
 html2text>=2016.9.19
 jinja2==3.1.4
 jsonschema==4.23.0
+jwt==1.3.1  # needed for allauth
 markdown==3.7
 nltk>=3.8.1,<4.0.0
 numpy==1.26.4