Update to the new cookiecutteR

.gitlab-ci.yml

@@ -9,6 +9,9 @@ stages:
 # === Variables ===
 
 variables:
+  PACKAGE_VERSION: "0.1.0"
+  DOCS_SECRET_KEY: "QQRcgz67PxJNFopTWGygv1Y9iqKle0Mb2rxFh22a9cc/"
+  # Notebook environment variables
   PYTHON_VERSION: "3.6"
   SPARK_MASTER: "spark://192.168.6.210:7077"
   SPARK_ARGS:
@@ -20,50 +23,46 @@ variables:
   DB_PORT: "8331"
 
 
-# === Conda ===
-
-.conda_configure: &conda_configure
-  before_script:
-    # Conda configure
-    - conda config --append channels bioconda
-    - conda config --append channels ostrokach-forge
-    - conda config --append channels kimlab
-    - conda config --append channels ostrokach
-
-
 # === Pages ===
 
-.docs: &docs
+pages:
   stage: test
+  before_script:
+    # Create conda environment
+    # (nice to use an environment in case we use `gitlab-runner exec shell`)
+    - conda remove -n pages --all -yq || true
+    - conda create -n pages -yq || true
+    - conda install -n pages -yq
+      git python pip ipython jupyter ipykernel pypandoc
+    - source activate pages
+    # Install pip packages
+    - pip install -q
+      git+https://github.com/arximboldi/sinusoidal-sphinx-theme.git
+      sphinx sphinx_rtd_theme guzzle_sphinx_theme recommonmark
   script:
-    - conda install -yq jupyter nbconvert jupyter_contrib_nbextensions IPython ipykernel pandoc
-    - pip install -q sphinx sphinx_rtd_theme guzzle_sphinx_theme recommonmark nbsphinx
-    - mkdir -p docs/notebooks docs/_static/notebooks
-    - if [[ -e README.md ]] ; then 
-      sed 's|\.ipynb)|\.ipynb\.html)|g' README.md > docs/README.md ;
-      else echo "# README" > docs/README.md ;
-      fi
-    - (cd docs && ./convert_notebooks.sh)
+    # Generate notebooks.csv
+    - ./scripts/create_notebook_table.py -i notebooks/ -o docs/notebooks.csv
+    # Build pages
     - sphinx-build docs public/$DOCS_SECRET_KEY
-  after_script:
-    - if [[ -d /repo ]] ; then
-        sudo cp -rf public/* /repo/public ;
-        sudo chmod ugo+rwX -R /repo/public/* ;
-      fi
+    # Convert notebooks
+    - mkdir -p public/$DOCS_SECRET_KEY/notebooks
+    - ./scripts/convert_notebooks.sh notebooks/ public/$DOCS_SECRET_KEY/notebooks/
 
-test-pages:
-  <<: [*conda_configure, *docs]
-  except:
-    - master
-    - tags
 
-pages:
-  <<: [*conda_configure, *docs]
-  only:
-    - master
-    - tags
-  except:
-    - triggers
-  artifacts:
-    paths:
-    - public
+# === Deploy ===
+
+.exec-notebook: &exec-notebook
+  script:
+    - jupyter nbconvert "notebooks/{NOTEBOOK_NAME}.ipynb"
+      --to=html_ch
+      --output=$NOTEBOOK_NAME.html
+      --output-dir=logs/
+      --template=docs/output_toggle.tpl
+      --execute
+
+deploy:
+  stage: deploy
+  variables:
+    NOTEBOOK_NAME: deploy
+  <<: *exec-notebook
+  when: manual

AUTHORS.md

@@ -0,0 +1,9 @@
+# Credits
+
+## Development Lead
+
+- Alexey Strokach
+
+## Contributors
+
+None yet. Why not be the first?

CONTRIBUTING.md

@@ -0,0 +1,105 @@
+# Contributing
+
+Contributions are welcome, and they are greatly appreciated! Every
+little bit helps, and credit will always be given.
+
+You can contribute in many ways:
+
+## Types of Contributions
+
+### Report Bugs
+
+Report bugs at https://gitlab.com/biological-data-warehouse/adjacency-net/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+### Fix Bugs
+
+Look through the GitLab issues for bugs. Anything tagged with "bug"
+and "help wanted" is open to whoever wants to implement it.
+
+### Implement Features
+
+Look through the GitLab issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+### Write Documentation
+
+Adjacency Net could always use more documentation, whether as part of the
+official Adjacency Net docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+### Submit Feedback
+
+The best way to send feedback is to file an issue at https://gitlab.com/biological-data-warehouse/adjacency-net/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+## Get Started!
+
+Ready to contribute? Here's how to set up `adjacency-net` for local development.
+
+1. Fork the `adjacency-net` repo on GitLab.
+1. Clone your fork locally:
+
+    ```bash
+    git clone [email protected]:your_name_here/adjacency-net.git
+    ```
+
+1. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:
+
+    ```bash
+    mkvirtualenv adjacency-net
+    cd adjacency-net/
+    python setup.py develop
+    ```
+
+1. Create a branch for local development:
+
+    ```bash
+    git checkout -b name-of-your-bugfix-or-feature
+    ```
+
+    Now you can make your changes locally.
+
+1. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions:
+
+    ```bash
+    flake8 adjacency-net tests
+    python setup.py test or py.test
+    ```
+
+    To get flake8, just pip install them into your virtualenv.
+
+1. Commit your changes and push your branch to GitLab:
+
+    ```bash
+    git add .
+    git commit -m "Your detailed description of your changes."
+    git push origin name-of-your-bugfix-or-feature
+    ```
+
+1. Submit a pull request through the GitLab website.
+
+## Pull Request Guidelines
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+1. If the pull request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring, and add the
+   feature to the list in README.md.
+1. The pull request should work for all supported Python versions, as listed
+   in the [setup.py](setup.py) file.
+
+## Tips
+

HISTORY.md

@@ -0,0 +1,5 @@
+# History
+
+## 0.1.0 (2018-01-02)
+
+* First release.

LICENSE

@@ -0,0 +1,11 @@
+
+MIT License
+
+Copyright (c) 2018, Alexey Strokach
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+

README.md

@@ -0,0 +1,10 @@
+# Adjacency Net
+
+[![docs](https://img.shields.io/badge/docs-v0.1.0-blue.svg)](https://biological-data-warehouse.gitlab.io/adjacency-net/QQRcgz67PxJNFopTWGygv1Y9iqKle0Mb2rxFh22a9cc/)
+[![build status](https://gitlab.com/biological-data-warehouse/adjacency-net/badges/master/build.svg)](https://gitlab.com/biological-data-warehouse/adjacency-net/commits/master/)
+
+Neural network trained on protein sequences and adjacency matrices.
+
+## Features
+
+* TODO

docs/.gitignore

@@ -0,0 +1,3 @@
+/adjacency-net.rst
+/adjacency-net.*.rst
+/modules.rst