update pypi parser imports (#51)

* udpate pypi parser imports
Signed-off-by: vsoch <vsoch@users.noreply.github.com>

.github/CONTRIBUTING.md

@@ -4,10 +4,10 @@ This code is licensed under the MPL 2.0 [LICENSE](LICENSE).
 
 # Contributing
 
-When contributing to US-RSE Python, it is 
-important to properly communicate the gist of the contribution. 
-If it is a simple code or editorial fix, simply explaining this 
-within the GitHub Pull Request (PR) will suffice. But if this is a larger 
+When contributing to US-RSE Python, it is
+important to properly communicate the gist of the contribution.
+If it is a simple code or editorial fix, simply explaining this
+within the GitHub Pull Request (PR) will suffice. But if this is a larger
 fix or Enhancement, it should be first discussed with the project
 leader or developers.
 
@@ -26,8 +26,8 @@ Please note we have a code of conduct, and you should follow it.
 4. The project's default copyright and header have been included in any new
    source files.
 5. All (major) changes to must be documented in the "docs" folder.
-   If your PR changes a core functionality, please 
-   include clear description of the changes in your PR so that the docs 
+   If your PR changes a core functionality, please
+   include clear description of the changes in your PR so that the docs
    can be updated, or better, submit another PR to update the docs directly.
 6. If necessary, update the README.md.
 7. The pull request will be reviewed by others, and the final merge must be

.github/ISSUE_TEMPLATE/documentation-or-tutorial-request.md

@@ -3,5 +3,3 @@ name: Documentation or Tutorial Request
 about: What can we explain better, or what issue did you find?
 
 ---
-
-

.github/ISSUE_TEMPLATE/question.md

@@ -3,5 +3,3 @@ name: Question
 about: What's on your mind?
 
 ---
-
-

.github/dev-requirements.txt

@@ -0,0 +1,4 @@
+pre-commit
+black
+isort
+flake8

.github/workflows/build-deploy.yaml

@@ -3,15 +3,15 @@ name: Build Deploy Containers
 on:
   # Publish packages on release
   release:
-    types: [published] 
+    types: [published]
 
   pull_request: []
 
   # On push to main we build and deploy images
-  push: 
+  push:
     branches:
       - main
- 
+
 jobs:
   build:
     permissions:
@@ -29,7 +29,7 @@ jobs:
 
       - name: GHCR Login
         if: (github.event_name != 'pull_request')
-        uses: docker/login-action@v1 
+        uses: docker/login-action@v1
         with:
           registry: ghcr.io
           username: ${{ github.actor }}

.github/workflows/main.yml

@@ -11,58 +11,27 @@ jobs:
   formatting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - name: Setup black linter
-        run: conda create --quiet --name black pyflakes
-
+      - uses: actions/checkout@v3
       - name: Check Spelling
         uses: crate-ci/typos@592b36d23c62cb378f6097a292bc902ee73f93ef # version 1.0.4
         with:
           files: ./docs/getting_started/ ./docs/index.rst ./README.md
 
-      - name: Lint python code
-        run: |
-          export PATH="/usr/share/miniconda/bin:$PATH"
-          source activate black
-          pip install black
-          black --check citelang
-          
-      - name: Check imports with pyflakes
+      - name: Lint and format Python code
         run: |
-          export PATH="/usr/share/miniconda/bin:$PATH"
-          source activate black
-          pyflakes citelang/*.py
-          pyflakes citelang/client
-          pyflakes citelang/main/*.py
-          pyflakes citelang/main/badge/*.py
-          pyflakes citelang/utils/fileio.py
-          pyflakes citelang/utils/terminal.py
-          pyflakes citelang/main/graph/base.py
-          pyflakes citelang/main/graph/text.py
-          pyflakes citelang/main/graph/tree.py
-          pyflakes citelang/main/graph/cypher.py
-          pyflakes citelang/main/graph/dot.py
-          pyflakes citelang/main/graph/gexf.py
-          pyflakes citelang/main/graph/graph.py
-          pyflakes citelang/main/packages
-          pyflakes citelang/tests
+          pip install -r .github/dev-requirements.txt
+          pre-commit run --all-files
 
   testing:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-
-      - name: Setup black linter
-        run: conda create --quiet --name testing pytest
-
+      - uses: actions/checkout@v3
       - name: Run Tests
         env:
           CITELANG_LIBRARIES_KEY: ${{ secrets.CITELANG_LIBRARIES_KEY }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          export PATH="/usr/share/miniconda/bin:$PATH"
-          source activate testing
-          pip install -e .[all]
+          pip install .[all]
           pip install bs4
           cd citelang/tests
           /bin/bash test_client.sh

.github/workflows/release.yaml

@@ -23,7 +23,7 @@ jobs:
 
     - name: Build and publish
       env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USER }} 
+        TWINE_USERNAME: ${{ secrets.PYPI_USER }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASS }}
       run: |
         export PATH="/usr/share/miniconda/bin:$PATH"
@@ -35,7 +35,7 @@ jobs:
       uses: vsoch/citelang/action/gen@main
       env:
         CITELANG_LIBRARIES_KEY: ${{ secrets.CITELANG_LIBRARIES_KEY }}
-      with:   
+      with:
         package: citelang
         manager: pypi
         outfile: software-credit.md
@@ -45,7 +45,7 @@ jobs:
       uses: vsoch/citelang/action/badge@main
       env:
         CITELANG_LIBRARIES_KEY: ${{ secrets.CITELANG_LIBRARIES_KEY }}
-      with:   
+      with:
         package: citelang
         manager: pypi
         outfile: docs/assets/img/pypi-citelang.png

.github/workflows/test-action.yml

@@ -9,51 +9,51 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install CiteLang
-        run: pip install -e .[all]
+        run: pip install .[all]
 
       - name: Clone Repository
         run: git clone https://github.com/singularityhub/singularity-hpc /tmp/shpc
 
       - name: Test CiteLang Contrib
         uses: ./action/contrib
-        with:   
+        with:
           root: /tmp/shpc
           outdir: /tmp/shpc/.contrib
           start: 0.0.52
           end: 0.0.53
           detail: true
 
       - name: Ensure cache is populated
-        run: tree .contrib/cache
+        run: tree /tmp/shpc/.contrib/cache
 
       - name: Test CiteLang Released
         uses: vsoch/citelang/action/gen@main
         env:
           CITELANG_LIBRARIES_KEY: ${{ secrets.CITELANG_LIBRARIES_KEY }}
-        with:   
+        with:
           package: citelang
           manager: pypi
           outfile: software-credit.md
 
-      - name: Test citelang gen      
+      - name: Test citelang gen
         uses: ./action/gen
         env:
           CITELANG_LIBRARIES_KEY: ${{ secrets.CITELANG_LIBRARIES_KEY }}
-        with:   
+        with:
           package: citelang
           manager: pypi
           outfile: citelang.md
 
       - name: View generated file
         run: cat citelang.md
-        
+
       - name: Test citelang badge
         uses: ./action/badge
         env:
           CITELANG_LIBRARIES_KEY: ${{ secrets.CITELANG_LIBRARIES_KEY }}
-        with:   
+        with:
           package: citelang
           manager: pypi

.github/workflows/update-contributors.yaml

@@ -13,12 +13,12 @@ jobs:
       - name: Checkout Repository
         uses: actions/checkout@v2
       - name: Tributors Update
-      
+
         # Important! Update to release https://github.com/con/tributors
         uses: con/tributors@0.0.20
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:        
+        with:
 
           # Single text list (space separated) of parsers, leave unset to auto-detect
           parsers: unset

.pre-commit-config.yaml

@@ -0,0 +1,32 @@
+exclude: ".all-contributorsrc"
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: mixed-line-ending
+
+  - repo: local
+    hooks:
+      - id: black
+        name: black
+        language: python
+        types: [python]
+        entry: black
+
+      - id: isort
+        name: isort
+        args: [--filter-files]
+        language: python
+        types: [python]
+        entry: isort
+
+      - id: flake8
+        name: flake8
+        language: python
+        types: [python]
+        entry: flake8

CHANGELOG.md

@@ -14,6 +14,7 @@ and **Merged pull requests**. Critical items to know are:
 The versions coincide with releases on pip. Only major versions will be released as tags on GitHub.
 
 ## [0.0.x](https://github.com/vsoch/citelang/tree/main) (0.0.x)
+ - updates for pypi parsing (0.0.34)
  - release for joss paper (0.0.33)
  - spack changed their packages url (0.0.32)
  - removing deprecated pypi argument and adding from_file to package base (0.0.31)

CITATION.cff

@@ -8,4 +8,3 @@ title: "CiteLang: Modeling the Research Software Ecosystem"
 version: 0.0.33
 doi: 10.21105/joss.04458
 date-released: 2022-09-04
-

README.md

@@ -18,9 +18,9 @@ software engineers we also want to move away from the traditional "be valued lik
 We are getting software metadata and a reference to an identifier via a package manager. This means
 that when you publish your software, you should publish it to an appropriate package manager.
 
-## Getting Started 
+## Getting Started
 
-If you want to use CiteLang as an analysis library, jump into the more detailed ⭐️ [Documentation](https://vsoch.github.io/citelang) ⭐️ 
+If you want to use CiteLang as an analysis library, jump into the more detailed ⭐️ [Documentation](https://vsoch.github.io/citelang) ⭐️
 or look specifically at the [Python API](https://vsoch.github.io/citelang/getting_started/user-guide.html#python).
 As an example analysis, the [RSEPedia Software Ecosystem](https://rseng.github.io/rsepedia-analysis/) is a completed automated setup that parses and summarizes dependencies across the [Research Software Encyclopedia](https://rseng.github.io/software) weekly, and it's powered by CiteLang! You can do similar analyses or build your own tools using CiteLang. We will provide a small summary of the tools available here.
 
@@ -67,7 +67,7 @@ The functionality that originally derived the name - a "markdown syntax for cita
 
 ## Contributors
 
-We use the [all-contributors](https://github.com/all-contributors/all-contributors) 
+We use the [all-contributors](https://github.com/all-contributors/all-contributors)
 tool to generate a contributors graphic below.
 
 <!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
@@ -82,7 +82,7 @@ tool to generate a contributors graphic below.
     </tr>
   </tbody>
   <tfoot>
-    
+
   </tfoot>
 </table>