Merge branch 'main' into mandd/LML_graphdump

.github/ISSUE_TEMPLATE.md

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+--------
+Issue Description
+--------
+##### What did you expect to see happen?
+
+
+##### What did you see instead?
+
+
+##### Do you have a suggested fix for the development team?
+
+
+##### Please attach the input file(s) that generate this error.  The simpler the input, the faster we can find the issue.
+
+
+
+----------------
+For Change Control Board: Issue Review
+----------------
+This review should occur before any development is performed as a response to this issue.
+- [ ] 1. Is it tagged with a type: defect or task?
+- [ ] 2. Is it tagged with a priority: critical, normal or minor?
+- [ ] 3. If it will impact requirements or requirements tests, is it tagged with requirements?
+- [ ] 4. If it is a defect, can it cause wrong results for users? If so an email needs to be sent to the users.
+- [ ] 5. Is a rationale provided? (Such as explaining why the improvement is needed or why current code is wrong.)
+
+-------
+For Change Control Board: Issue Closure
+-------
+This review should occur when the issue is imminently going to be closed.
+- [ ] 1. If the issue is a defect, is the defect fixed?
+- [ ] 2. If the issue is a defect, is the defect tested for in the regression test system?  (If not explain why not.)
+- [ ] 3. If the issue can impact users, has an email to the users group been written (the email should specify if the defect impacts stable or master)?
+- [ ] 4. If the issue is a defect, does it impact the latest release branch? If yes, is there any issue tagged with release (create if needed)?
+- [ ] 5. If the issue is being closed without a pull request, has an explanation of why it is being closed been provided?

.github/ISSUE_TEMPLATE/defect-report.yml

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+name: Defect Report
+description: Report a DEFECT you experienced using the code
+title: "[DEFECT] "
+labels: defect, priority_normal
+body:
+  - type: checkboxes
+    id: requirements
+    attributes:
+      label: Thank you for the defect report
+      description: Please check the suggestions below before proceeding
+      options:
+        - label: I am using the latest version.
+          required: true
+        - label: |
+            I have created a [minimum, reproducible example](https://stackoverflow.com/help/minimal-reproducible-example)
+            that demonstrates the defect.
+  - type: textarea
+    id: defect-description
+    attributes:
+      label: Defect Description
+      description: A clear and concise description of what the defect is.
+    validations:
+      required: true
+  - type: textarea
+    id: steps-to-reproduce
+    attributes:
+      label: Steps to Reproduce
+      description: Describe how to reproduce the defect.
+    validations:
+      required: true
+  - type: textarea
+    id: expected-behavior
+    attributes:
+      label: Expected Behavior
+      description: A clear and concise description of what you expected to happen.
+    validations:
+      required: true
+  - type: textarea
+    id: additional-info
+    attributes:
+      label: Screenshots and Input Files
+      description: Please attach any additional information like input files, screenshots, recordings and logs, etc.
+    validations:
+      required: false
+  - type: dropdown
+    id: which-os
+    attributes:
+      label: OS
+      description: Which OS are you using?
+      options:
+        - Linux
+        - MacOS
+        - Windows
+    validations:
+      required: true
+  - type: input
+    id: which-version
+    attributes:
+      label: OS Version
+      description: Which OS version are you using?
+      placeholder: "10.15.5"
+    validations:
+      required: false
+  - type: dropdown
+    id: which-package-manager
+    attributes:
+      label: Dependency Manager
+      description: Which Dependency Manager are you using?
+      options:
+        - PIP
+        - CONDA
+    validations:
+      required: true
+  - type: checkboxes
+    id: issue-review
+    attributes:
+      label: "For Change Control Board: Issue Review"
+      description: "This review should occur before any development is performed as a response to this issue."
+      options:
+        - label: "Is it tagged with a type: defect or task?"
+        - label: "Is it tagged with a priority: critical, normal or minor?"
+        - label: "If it will impact requirements or requirements tests, is it tagged with requirements?"
+        - label: "If it is a defect, can it cause wrong results for users? If so an email needs to be sent to the users."
+        - label: "Is a rationale provided? (Such as explaining why the improvement is needed or why current code is wrong.)"
+  - type: checkboxes
+    id: issue-closure
+    attributes:
+      label: "For Change Control Board: Issue Closure"
+      description: "This review should occur when the issue is imminently going to be closed."
+      options:
+        - label: "If the issue is a defect, is the defect fixed?"
+        - label: "If the issue is a defect, is the defect tested for in the regression test system?  (If not explain why not.)"
+        - label: "If the issue can impact users, has an email to the users group been written (the email should specify if the defect impacts stable or master)?"
+        - label: "If the issue is a defect, does it impact the latest release branch? If yes, is there any issue tagged with release (create if needed)?"
+        - label: "If the issue is being closed without a pull request, has an explanation of why it is being closed been provided?"

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest a new capability or addition you would like to see
+title: "[TASK] Title here"
+labels: priority_minor, task
+assignees:
+
+
+---
+
+--------
+Issue Description
+--------
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+----------------
+For Change Control Board: Issue Review
+----------------
+This review should occur before any development is performed as a response to this issue.
+- [ ] 1. Is it tagged with a type: defect or task?
+- [ ] 2. Is it tagged with a priority: critical, normal or minor?
+- [ ] 3. If it will impact requirements or requirements tests, is it tagged with requirements?
+- [ ] 4. If it is a defect, can it cause wrong results for users? If so an email needs to be sent to the users.
+- [ ] 5. Is a rationale provided? (Such as explaining why the improvement is needed or why current code is wrong.)
+
+-------
+For Change Control Board: Issue Closure
+-------
+This review should occur when the issue is imminently going to be closed.
+- [ ] 1. If the issue is a defect, is the defect fixed?
+- [ ] 2. If the issue is a defect, is the defect tested for in the regression test system?  (If not explain why not.)
+- [ ] 3. If the issue can impact users, has an email to the users group been written (the email should specify if the defect impacts stable or master)?
+- [ ] 4. If the issue is a defect, does it impact the latest release branch? If yes, is there any issue tagged with release (create if needed)?
+- [ ] 5. If the issue is being closed without a pull request, has an explanation of why it is being closed been provided?

.github/ISSUE_TEMPLATE/under-discussion.md

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+---
+name: Under Discussion
+about: This issue template is aimed to propose an item of discussion for new features
+  or similar
+title: "[UNDER-DISCUSSION] New Topic"
+labels: under-discussion
+assignees:
+
+
+---
+
+--------
+Under Discussion Topic
+--------
+
+**Summary of the topic to be discussed with the development team**
+A clear and concise description of the topic to be discusses
+
+**Describe the solution you'd like to be implemented**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+----------------
+For Change Control Board: Issue Review
+----------------
+This review should occur before any development is performed as a response to this issue.
+- [ ] 1. Is it tagged with the under_discussion type?
+- [ ] 2. If implemented, it will add a new requirement?
+- [ ] 3. Is a rationale provided? (Such as explaining why the improvement is needed )
+
+-------
+For Change Control Board: Issue Closure
+-------
+This review should occur when the issue is imminently going to be closed.
+- [ ] 1. The discussion determined the addition of a new ```task``` issue?

.github/PULL_REQUEST_TEMPLATE.md

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+--------
+Pull Request Description
+--------
+##### What issue does this change request address? (Use "#" before the issue to link it, i.e., #42.)
+
+
+##### What are the significant changes in functionality due to this change request?
+
+
+----------------
+For Change Control Board: Change Request Review
+----------------
+The following review must be completed by an authorized member of the Change Control Board.
+- [ ] 1. Review all computer code.
+- [ ] 2. If any changes occur to the input syntax, there must be an accompanying change to the user manual and xsd schema. If the input syntax change deprecates existing input files, a conversion script needs to be added (see Conversion Scripts).
+- [ ] 3. Make sure the Python code and commenting standards are respected.
+- [ ] 4. Automated Tests should pass.
+- [ ] 5. If significant functionality is added, there must  be tests added to check this. Tests should cover all possible options.  Multiple short tests are preferred over one large test.
+- [ ] 6. If the change modifies or adds a requirement or a requirement based test case, the Change Control Board's Chair or designee also needs to approve the change.  The requirements and the requirements test shall be in sync.
+- [ ] 7. The merge request must reference an issue.  If the issue is closed, the issue close checklist shall be done.
+

.github/workflows/github-actions.yml

@@ -0,0 +1,94 @@
+name: GitHub DACKAR test
+run-name: ${{ github.actor }} is testing out DACKAR
+on: [push, pull_request]
+
+concurrency:
+  # Here the group is defined by the head_ref of the PR
+  group: ${{ github.head_ref }}
+  # Here we specify that we'll cancel any "in progress" workflow of the same group. Thus if we push, ammend a commit and push
+  # again the previous workflow will be cancelled, thus saving us github action build minutes and avoid any conflicts
+  cancel-in-progress: true
+
+jobs:
+  Test-DACKAR-Linux:
+    # runs-on: [self-hosted, ubuntu-latest]
+    # runs-on: ${{ fromJSON('["ubuntu-latest", "self-hosted"]')[github.repository == 'github/docs-internal'] }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: "latest"
+          channels: conda-forge, defaults
+          use-only-tar-bz2: true  # IMPORTANT: This needs to be set for caching to work properly!
+          auto-update-conda: true
+          auto-activate-base: true
+      - run: echo " The job was automatically triggered by a ${{ github.event_name }} event."
+      - run: echo " This job is now running on a ${{ runner.os }} server"
+      - run: echo " The name of your branch is ${{ github.ref }} and your repository is ${{ github.repository }}."
+      - name: Check out repository code
+        uses: actions/checkout@v3
+      - run: pwd
+      - run: |
+          conda create -n dackar_libs python=3.11
+          conda init bash && source ~/.bashrc && conda activate dackar_libs
+          pip install spacy==3.5 textacy matplotlib nltk coreferee beautifulsoup4 networkx pysbd tomli numerizer autocorrect pywsd openpyxl quantulum3[classifier] numpy==1.26 scikit-learn pyspellchecker contextualSpellCheck pandas
+          python3 -m spacy download en_core_web_lg
+          python3 -m coreferee install en
+          python3 -m nltk.downloader all
+
+
+  Test-DACKAR-Macos:
+    runs-on: macos-latest
+    steps:
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: "latest"
+          channels: conda-forge, defaults
+          use-only-tar-bz2: true  # IMPORTANT: This needs to be set for caching to work properly!
+          auto-update-conda: true
+          auto-activate-base: true
+      - run: echo " The job was automatically triggered by a ${{ github.event_name }} event."
+      - run: echo " This job is now running on a ${{ runner.os }} server"
+      - run: echo " The name of your branch is ${{ github.ref }} and your repository is ${{ github.repository }}."
+      - name: Check out repository code
+        uses: actions/checkout@v3
+      - run: pwd
+      - run: |
+          conda create -n dackar_libs python=3.11
+          conda init zsh && source ~/.zshrc && conda activate dackar_libs
+          pip install spacy==3.5 textacy matplotlib nltk coreferee beautifulsoup4 networkx pysbd tomli numerizer autocorrect pywsd openpyxl quantulum3[classifier] numpy==1.26 scikit-learn pyspellchecker contextualSpellCheck pandas
+          python3 -m spacy download en_core_web_lg
+          python3 -m coreferee install en
+          python3 -m nltk.downloader all
+
+
+  Test-DACKAR-Windows:
+    runs-on: windows-latest
+    steps:
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: "latest"
+          channels: conda-forge, defaults
+          use-only-tar-bz2: true  # IMPORTANT: This needs to be set for caching to work properly!
+          activate-environment: dackar_libs
+          auto-update-conda: true
+          auto-activate-base: false
+      - run: echo " The job was automatically triggered by a ${{ github.event_name }} event."
+      - run: echo " This job is now running on a ${{ runner.os }} server"
+      - run: echo " The name of your branch is ${{ github.ref }} and your repository is ${{ github.repository }}."
+      - name: Check out repository code
+        uses: actions/checkout@v3
+      - run: pwd
+      - run: |
+          echo " Create dackar_libs"
+          conda install python=3.11
+          echo " Conda information"
+          conda info
+          echo " Activate Dackar conda environment"
+          pip install spacy==3.5 textacy matplotlib nltk coreferee beautifulsoup4 networkx pysbd tomli numerizer autocorrect pywsd openpyxl quantulum3[classifier] numpy==1.26 scikit-learn pyspellchecker contextualSpellCheck pandas
+          conda list
+          which python
+          python -m spacy download en_core_web_lg
+          python -m coreferee install en
+          python -m nltk.downloader all
+

.github/workflows/sphinx.yml

@@ -0,0 +1,54 @@
+name: "Sphinx: Render docs"
+
+on: push
+
+jobs:
+  build:
+    # runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: "latest"
+          channels: conda-forge, defaults
+          use-only-tar-bz2: true  # IMPORTANT: This needs to be set for caching to work properly!
+          auto-update-conda: true
+          activate-environment: dackar_libs
+          auto-activate-base: false
+      # - name: Use Pandoc
+      #   uses: docker://pandoc/core:2.9
+      #   with:
+      #     args: "--help" # gets appended to pandoc command
+      - name: Install
+        uses: pandoc/actions/setup@v1
+        with:
+          version: 2.19
+
+      - name: Run pandoc
+        run: pandoc --version
+      - run: echo " Install Libraries Required to build Sphinx Documents"
+      - run: |
+          pwd
+          ls -l
+          pip install sphinx sphinx_rtd_theme nbsphinx sphinx-copybutton sphinx-autoapi
+          cd docs
+          make html
+          cd ..
+      # - name: Build HTML
+      #   uses: ammaraskar/sphinx-action@master
+      #   with:
+      #     pre-build-command: "apt-get update && apt-get install -y pandoc"
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: html-docs
+          path: docs/_build/html/
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        if: github.ref == 'refs/heads/main'
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/_build/html