updated doctrings, black, and version bump (#85)

* updated doctrings, black, and version bump Signed-off-by: vsoch <[email protected]> * update container base to bookworm Signed-off-by: vsoch <[email protected]> --------- Signed-off-by: vsoch <[email protected]> Co-authored-by: vsoch <[email protected]>
rseng · Oct 22, 2023 · 322a123 · 322a123
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -12,7 +12,7 @@ jobs:
   formatting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Setup black environment
         run: conda create --quiet --name black pyflakes
@@ -21,7 +21,7 @@ jobs:
         run: |
           export PATH="/usr/share/miniconda/bin:$PATH"
           source activate black
-          pip install black
+          pip install black==23.3.0
           black --check rse
 
       - name: Check imports with pyflakes
@@ -38,7 +38,7 @@ jobs:
     env:
       RSE_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Setup testing environment
         run: conda create --quiet --name testing pytest
 
@@ -56,7 +56,7 @@ jobs:
     env:
       CONTAINER: quay.io/vanessa/rse
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Build Docker Image
         run: docker build -t "${CONTAINER}" .
       - name: Tag and Preview Container

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,7 @@ and **Merged pull requests**. Critical items to know are:
 The versions coincide with releases on pip.
 
 ## [0.0.x](https://github.com/rseng/rse/tree/master) (0.0.x)
+ - allow an erroneous response for GitHub org get repos (0.0.48)
  - allow custom import for csv and google-sheet (0.0.47)
  - support for csv import (0.0.46)
  - ensure Google scraper skips malformed rows, etc (0.0.45)

diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,5 @@
-FROM bitnami/minideb:stretch
+FROM bitnami/minideb:bookworm
+
 # docker build -t quay.io/vanessa/rse .
 LABEL MAINTAINER @vsoch
 ENV PATH /opt/conda/bin:${PATH}

diff --git a/rse/__init__.py b/rse/__init__.py
@@ -1,13 +1,3 @@
-"""
-
-Copyright (C) 2020-2022 Vanessa Sochat.
-
-This Source Code Form is subject to the terms of the
-Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
-with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-"""
-
 from .version import __version__
 
 assert __version__
diff --git a/rse/app/api.py b/rse/app/api.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2020-2022 Vanessa Sochat.
+Copyright (C) 2020-2023 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed

diff --git a/rse/app/config.py b/rse/app/config.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2020-2022 Vanessa Sochat.
+Copyright (C) 2020-2023 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed

diff --git a/rse/app/export.py b/rse/app/export.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2020-2022 Vanessa Sochat.
+Copyright (C) 2020-2023 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -157,7 +157,6 @@ def kill():
         )
 
     for url, outfile in urls.items():
-
         # Skip if we've already created it
         if os.path.exists(outfile):
             continue

diff --git a/rse/app/server.py b/rse/app/server.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2020-2022 Vanessa Sochat.
+Copyright (C) 2020-2023 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed

diff --git a/rse/app/views/main.py b/rse/app/views/main.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2020-2022 Vanessa Sochat.
+Copyright (C) 2020-2023 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -33,11 +33,9 @@ def index():
 
 @app.route("/")
 def topics_view():
-
     topics = app.client.topics()
     repos = []
     for name in app.client.list():
-
         # Obtain the repository and load the data.
         repo = app.client.get(name[0])
         repo.parser.load(repo.data)

diff --git a/rse/app/views/repositories.py b/rse/app/views/repositories.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2020-2022 Vanessa Sochat.
+Copyright (C) 2020-2023 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -18,7 +18,6 @@
 
 @app.route("%srepository/<path:uid>" % RSE_URL_PREFIX)
 def repository_view(uid):
-
     # Obtain the repository and load the data.
     repo = app.client.get(uid)
     repo.parser.load(repo.data)
@@ -55,7 +54,6 @@ def annotate_repos(message=""):
 
 @app.route("%sannotate-criteria" % RSE_URL_PREFIX, methods=["POST", "GET"])
 def annotate_criteria():
-
     # If it's a post, update the annotation
     username = None
     if request.method == "POST":
@@ -96,7 +94,6 @@ def annotate_criteria():
 
 @app.route("%srepository/<path:uid>/annotate-criteria" % RSE_URL_PREFIX)
 def annotate_static_criteria(uid):
-
     # Get criteria / annotation set for specific repository
     username = request.args.get("username")
     repo = app.client.get(uid)
@@ -115,7 +112,6 @@ def annotate_static_criteria(uid):
 
 @app.route("%srepository/<path:uid>/annotate-taxonomy" % RSE_URL_PREFIX)
 def annotate_static_taxonomy(uid):
-
     # Get criteria / annotation set for specific repository
     username = request.args.get("username")
     repo = app.client.get(uid)
@@ -137,7 +133,6 @@ def annotate_static_taxonomy(uid):
 
 @app.route("%sannotate-taxonomy" % RSE_URL_PREFIX, methods=["GET", "POST"])
 def annotate_taxonomy():
-
     # If we don't have a color lookup, make one
     if not hasattr(app, "taxonomy"):
         app.taxonomy = generate_taxonomy(app)
@@ -181,7 +176,6 @@ def annotate_taxonomy():
 
 
 def generate_taxonomy(app):
-
     taxonomy = app.client.list_taxonomy()
 
     # Update the color list with existing colors (consistency)
@@ -209,7 +203,6 @@ def generate_taxonomy(app):
 
 
 def update_criteria():
-
     updates = {}
     repo_uid = request.form.get("repo_uid")
     username = request.form.get("username")
@@ -231,7 +224,6 @@ def update_criteria():
 
 
 def update_taxonomy():
-
     uids = []
     repo_uid = request.form.get("repo_uid")
     username = request.form.get("username")

diff --git a/rse/client/__init__.py b/rse/client/__init__.py
@@ -2,7 +2,7 @@
 
 """
 
-Copyright (C) 2020 Vanessa Sochat.
+Copyright (C) 2020-2023 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed

diff --git a/rse/client/add.py b/rse/client/add.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2020 Vanessa Sochat.
+Copyright (C) 2020-2023 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -14,7 +14,6 @@
 
 
 def main(args, extra):
-
     # Create a research software encyclopedia
     enc = Encyclopedia(config_file=args.config_file, database=args.database)
 

diff --git a/rse/client/annotate.py b/rse/client/annotate.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2020 Vanessa Sochat.
+Copyright (C) 2020-2023 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -13,7 +13,6 @@
 
 
 def main(args, extra):
-
     # Create a research software encyclopedia
     client = Encyclopedia(config_file=args.config_file, database=args.database)
 

diff --git a/rse/client/clear.py b/rse/client/clear.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2020 Vanessa Sochat.
+Copyright (C) 2020-2023 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -12,7 +12,6 @@
 
 
 def main(args, extra):
-
     # Clear a parser, uid, or target
     enc = Encyclopedia(config_file=args.config_file, database=args.database)
     enc.clear(args.target, noprompt=args.force)
diff --git a/rse/client/config.py b/rse/client/config.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2020 Vanessa Sochat.
+Copyright (C) 2020-2023 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -17,7 +17,6 @@
 
 
 def main(args, extra):
-
     bot = logging.getLogger("rse.client")
 
     # The user wants to set the database

diff --git a/rse/client/exists.py b/rse/client/exists.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2020-2022 Vanessa Sochat.
+Copyright (C) 2020-2023 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -16,7 +16,6 @@
 
 
 def main(args, extra):
-
     enc = Encyclopedia(config_file=args.config_file)
 
     # Case 1: empty list indicates listing all

diff --git a/rse/client/export.py b/rse/client/export.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2020-2022 Vanessa Sochat.
+Copyright (C) 2020-2023 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -19,7 +19,6 @@
 
 
 def main(args, extra):
-
     client = Encyclopedia(config_file=args.config_file, database=args.database)
 
     # Case 1: empty list indicates listing all
@@ -28,7 +27,6 @@ def main(args, extra):
 
     # Export a list of repos
     if args.export_type == "repos-txt":
-
         # We just want the unique id, the first result
         repos = [x[0] for x in client.list()]
         write_file("\n".join(repos), args.path)

diff --git a/rse/client/generate.py b/rse/client/generate.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2020-2022 Vanessa Sochat.
+Copyright (C) 2020-2023 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -13,7 +13,6 @@
 
 
 def main(args, extra):
-
     punctuation = "!#$%&()*+,-./:;<=>?@^_{|}~"
     choices = string.ascii_letters + string.digits + punctuation
     selected = [random.SystemRandom().choice(choices) for _ in range(50)]

diff --git a/rse/client/get.py b/rse/client/get.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2020-2022 Vanessa Sochat.
+Copyright (C) 2020-2023 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -18,7 +18,6 @@
 
 
 def main(args, extra):
-
     # Create a research software encyclopedia
     enc = Encyclopedia(config_file=args.config_file, database=args.database)
 

diff --git a/rse/client/imp.py b/rse/client/imp.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2022 Vanessa Sochat.
+Copyright (C) 2020-2023 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -20,7 +20,6 @@ def parse_extra(extra):
     args = []
     kwargs = {}
     for arg in extra:
-
         # This is a key value pair (extra)
         if arg.startswith("--") and "=" in arg:
             key, val = arg.strip().split("=")
@@ -33,7 +32,6 @@ def parse_extra(extra):
 
 
 def main(args, extra):
-
     try:
         importer = get_importer(args.import_type)
     except:

diff --git a/rse/client/init.py b/rse/client/init.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2020-2022 Vanessa Sochat.
+Copyright (C) 2020-2023 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -15,7 +15,6 @@
 
 
 def main(args, extra):
-
     # present working directory
     path = args.path
     if args.path == ".":

diff --git a/rse/client/label.py b/rse/client/label.py
@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2020-2022 Vanessa Sochat.
+Copyright (C) 2020-2023 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -12,7 +12,6 @@
 
 
 def main(args, extra):
-
     enc = Encyclopedia(config_file=args.config_file, database=args.database)
 
     # Grab the repository uid, label key and value