update structure

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,38 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**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.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/ci.yml

@@ -0,0 +1,20 @@
+name: CI
+on: push
+jobs:
+  quality:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.8"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff black
+      # Include `--format=github` to enable automatic inline annotations.
+      # - name: Check linters
+      #   run: ruff --format=github .  # ruff does not allow trailing white space in logo (cli.py)
+      - name: Check format
+        run: black --check .

.github/workflows/docker.yml

@@ -0,0 +1,58 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# GitHub recommends pinning actions to a commit SHA.
+# To get a newer version, you will need to update the SHA.
+# You can also reference a tag or branch, but the action may change without warning.
+
+name: Publish Docker image
+
+on:
+  release:
+    types: [published]
+
+  push:
+    branches:
+      - main
+
+jobs:
+  push_to_registries:
+    name: Push Docker image to multiple registries
+    runs-on: ubuntu-latest
+    permissions:
+      packages: write
+      contents: read
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v3
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.API_GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: |
+            robaina/pynteny
+            ghcr.io/${{ github.repository }}
+      
+      - name: Build and push Docker images
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/docs.yml

@@ -0,0 +1,21 @@
+name: docs
+on:
+  push:
+    branches: [ main ]
+    paths:
+      - 'docs/**'
+      - 'mkdocs.yml'
+
+jobs:
+
+  build-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v2
+      - run: pip install --upgrade pip && pip install mkdocs mkdocs-gen-files pymdown-extensions mkdocs-jupyter mkdocstrings[python]
+      - run: git config user.name 'github-actions[bot]' && git config user.email 'github-actions[bot]@users.noreply.github.com'
+      - name: Publish docs
+        run: mkdocs gh-deploy

.github/workflows/draft-pdf.yml → .github/workflows/joss.yml

@@ -1,3 +1,4 @@
+name: joss
 on: [push]
 
 jobs:
@@ -6,18 +7,18 @@ jobs:
     name: Paper Draft
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Open Journals PDF Generator
         uses: openjournals/openjournals-draft-action@master
         with:
           journal: joss
           # This should be the path to the paper within your repo.
-          paper-path: paper/paper.md
+          paper-path: ms/paper.md
       - name: Upload
         uses: actions/upload-artifact@v1
         with:
           name: paper
           # This is the output path where Pandoc will write the compiled
           # PDF. Note, this should be the same directory as the input
           # paper.md
-          path: paper/paper.pdf
+          path: ms/paper.pdf

.github/workflows/tests.yml

@@ -0,0 +1,57 @@
+name: tests
+on:
+  push:
+    branches: [ main ]
+    paths-ignore:
+      - '**.md'
+      - '**.ipynb'
+      - '**.bib'
+      - 'ms/*'
+  pull_request:
+    types: [opened, reopened, edited]
+    paths-ignore:
+      - '**.md'
+      - '**.ipynb'
+      - '**.bib'
+      - 'ms/*'
+
+jobs:
+
+  create-env:
+    name: ${{ matrix.os }} 
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+
+    steps:
+      - name: checkout repository
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: create environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: 3.8
+          # mamba-version: "*"
+          channels: conda-forge,bioconda,defaults
+          auto-activate-base: false
+          activate-environment: tests_pynteny
+          environment-file: envs/pynteny-dev.yml
+
+      - name: Build & Install Pynteny
+        run: poetry build && pip install dist/pynteny*.whl
+
+      - name: Run tests and collect coverage
+        run: pynteny --help && coverage run --omit pynteny/wrappers.py,pynteny/cli.py,pynteny/subcommands.py,pynteny/utils.py -m unittest discover tests && coverage xml
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          version: "v0.1.15"

CONTRIBUTING.md

@@ -0,0 +1,80 @@
+# Contributing to BRENDApyrser
+
+First of all, thanks for taking the time to contribute! :tada::+1:
+
+Here you will find a set of guidelines for contributing to BRENDApyrser. Feel free to propose changes to this document in a pull request.
+
+## Code of conduct
+
+This project and everyone participating in it is governed by the [Contributor Covenant, v2.0](.github/CODE_OF_CONDUCT.md) code of conduct. By participating, you are expected to uphold this code.
+
+## I have a question!
+
+If you only have a question about all things related to BRENDApyrser, the best course of actions for you is to open a new [discussion](https://github.com/Robaina/BRENDApyrser/discussions).
+
+## How can I contribute?
+
+### 1. Reporting bugs
+
+We all make mistakes, and the developers behind BRENDApyrser are no exception... So, if you find a bug in the source code, please open an [issue](https://github.com/Robaina/BRENDApyrser/issues) and report it. Please, first search for similar issues that are currrently open.
+
+### 2. Suggesting enhancements
+
+Are you missing some feature that would like BRENDApyrser to have? No problem! You can contribute by suggesting an enhancement, just open a new issue and tag it with the [```enhancement```](https://github.com/Robaina/BRENDApyrser/labels/enhancement) label. Please, first search for similar issues that are currrently open.
+
+### 3. Improving the documentation
+
+Help is always needed at improving the [documentation](https://robaina.github.io/BRENDApyrser/). Either adding more detailed docstrings, usage explanations or new examples.
+
+## First contribution
+
+Unsure where to begin contributing to BRENDApyrser? You can start by looking for issues with the label [```good first issue```](https://github.com/Robaina/BRENDApyrser/labels/good%20first%20issue). If you are unsure about how to set a developer environment for BRENDApyrser, do take a look at the section below. Thanks!
+
+## Setting up a local developer environment
+
+To setup up a developer environment for BRENDApyrser:
+
+1. Fork and download repo, cd to downloaded directory. You should create a new branch to work on your issue.
+
+2. Create conda environment with required dependencies:
+
+The file `envs/BRENDApyrser-dev.yml` contains all dependencies required to use BRENDApyrser. Conda is very slow solving the environment. It is recommended to use [mamba](https://github.com/mamba-org/mamba) instead:
+
+```bash
+mamba env create -n BRENDApyrser-dev -f envs/BRENDApyrser-dev.yml
+conda activate BRENDApyrser-dev
+```
+
+3. Build package
+
+```bash
+(BRENDApyrser-dev) poetry build
+```
+
+4. Install BRENDApyrser
+
+```bash
+(BRENDApyrser-dev) pip install dist/BRENDApyrser*.whl
+```
+
+5. Run tests
+
+```bash
+(BRENDApyrser-dev) python -m unittest discover tests
+```
+
+## Building the documentation
+
+The documentation is formed by a series of markdown files located in directory [docs](https://github.com/Robaina/BRENDApyrser/tree/main/docs). This repo uses [mkdocs](https://www.mkdocs.org/) to automatically generate documentation pages from markdown files. Also, [MathJax](https://github.com/mathjax/MathJax) syntax is allowed!
+
+This means that, to modify the [API reference](https://robaina.github.io/BRENDApyrser/references/api/), all you need to do is to modify the docstring directly in the source file where the definion/class is located. And, to update the documentation pages, you just have to update the corresponding markdown file in the [docs](https://github.com/Robaina/BRENDApyrser/tree/main/docs) directory. Note that, if you need to change the documentation structure (e.g., add or new pages),you would need to tell mkdocs about this change through its [configuration file](https://github.com/Robaina/BRENDApyrser/blob/main/mkdocs.yml). Or just open an issue and ask for help!
+
+When all the changes are ready to deploy, just open a pull request. After reviewing and merging the changes, the documentation will be automatically deployed.
+
+Run the documentation locally with:
+
+> mkdocs serve
+
+## Tests on push and pull request to main
+
+BRENDApyrser's repo contains a [GitHub Action](https://github.com/features/actions) to perform build and integration tests which is triggered automatically on push and pull request events to the main brach. Currently the tests include building and installing BRENDApyrser in Ubuntu and MacOS and running the [test](tests) suit.