Use cookiecutter

.appveyor.yml

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+version: '{branch}-{build}'
+build: off
+environment:
+  global:
+  matrix:
+    - TOXENV: check
+      TOXPYTHON: C:\Python36\python.exe
+      PYTHON_HOME: C:\Python36
+      PYTHON_VERSION: '3.6'
+      PYTHON_ARCH: '32'
+    - TOXENV: py36
+      TOXPYTHON: C:\Python36\python.exe
+      PYTHON_HOME: C:\Python36
+      PYTHON_VERSION: '3.6'
+      PYTHON_ARCH: '32'
+    - TOXENV: py36
+      TOXPYTHON: C:\Python36-x64\python.exe
+      PYTHON_HOME: C:\Python36-x64
+      PYTHON_VERSION: '3.6'
+      PYTHON_ARCH: '64'
+    - TOXENV: py37
+      TOXPYTHON: C:\Python37\python.exe
+      PYTHON_HOME: C:\Python37
+      PYTHON_VERSION: '3.7'
+      PYTHON_ARCH: '32'
+    - TOXENV: py37
+      TOXPYTHON: C:\Python37-x64\python.exe
+      PYTHON_HOME: C:\Python37-x64
+      PYTHON_VERSION: '3.7'
+      PYTHON_ARCH: '64'
+init:
+  - ps: echo $env:TOXENV
+  - ps: ls C:\Python*
+install:
+  - '%PYTHON_HOME%\python -mpip install --progress-bar=off tox -rci/requirements.txt'
+  - '%PYTHON_HOME%\Scripts\virtualenv --version'
+  - '%PYTHON_HOME%\Scripts\easy_install --version'
+  - '%PYTHON_HOME%\Scripts\pip --version'
+  - '%PYTHON_HOME%\Scripts\tox --version'
+test_script:
+  - cmd /E:ON /V:ON /C .\ci\appveyor-with-compiler.cmd %PYTHON_HOME%\Scripts\tox
+on_failure:
+  - ps: dir "env:"
+  - ps: get-content .tox\*\log\*
+
+### To enable remote debugging uncomment this (also, see: http://www.appveyor.com/docs/how-to/rdp-to-build-worker):
+# on_finish:
+#   - ps: $blockRdp = $true; iex ((new-object net.webclient).DownloadString('https://raw.githubusercontent.com/appveyor/ci/master/scripts/enable-rdp.ps1'))

.bumpversion.cfg

@@ -0,0 +1,20 @@
+[bumpversion]
+current_version = 0.0.0
+commit = True
+tag = True
+
+[bumpversion:file:setup.py]
+search = 'fallback_version': '{current_version}'
+replace = 'fallback_version': '{new_version}'
+
+[bumpversion:file:README.rst]
+search = v{current_version}.
+replace = v{new_version}.
+
+[bumpversion:file:docs/conf.py]
+search = version = release = '{current_version}'
+replace = version = release = '{new_version}'
+
+[bumpversion:file:src/prednet/__init__.py]
+search = __version__ = '{current_version}'
+replace = __version__ = '{new_version}'

.cookiecutterrc

@@ -0,0 +1,70 @@
+# This file exists so you can easily regenerate your project.
+#
+# `cookiepatcher` is a convenient shim around `cookiecutter`
+# for regenerating projects (it will generate a .cookiecutterrc
+# automatically for any template). To use it:
+#
+#    pip install cookiepatcher
+#    cookiepatcher gh:ionelmc/cookiecutter-pylibrary project-path
+#
+# See:
+#    https://pypi.org/project/cookiepatcher
+#
+# Alternatively, you can run:
+#
+#    cookiecutter --overwrite-if-exists --config-file=project-path/.cookiecutterrc gh:ionelmc/cookiecutter-pylibrary
+
+default_context:
+
+    _extensions:               ['jinja2_time.TimeExtension']
+    _template:                 'cookiecutter-pylibrary/'
+    allow_tests_inside_package: 'yes'
+    appveyor:                  'yes'
+    c_extension_function:      'longest'
+    c_extension_module:        '_prednet'
+    c_extension_optional:      'no'
+    c_extension_support:       'no'
+    c_extension_test_pypi:     'no'
+    c_extension_test_pypi_username: 'coxlab'
+    ci_https_proxy:            'no'
+    codacy:                    'no'
+    codacy_projectid:          '[Get ID from https://app.codacy.com/app/coxlab/prednet/settings]'
+    codeclimate:               'no'
+    codecov:                   'no'
+    command_line_interface:    'argparse'
+    command_line_interface_bin_name: 'prednet'
+    coveralls:                 'no'
+    coveralls_token:           '[Required for Appveyor, take it from https://coveralls.io/github/coxlab/prednet]'
+    distribution_name:         'prednet'
+    email:                     '[email protected]'
+    full_name:                 'Bill Lotter'
+    landscape:                 'no'
+    license:                   'MIT license'
+    linter:                    'flake8'
+    package_name:              'prednet'
+    project_name:              'PredNet'
+    project_short_description: 'Code and models accompanying Deep Predictive Coding Networks for Video Prediction and Unsupervised Learning by Bill Lotter, Gabriel Kreiman, and David Cox. The PredNet is a deep recurrent convolutional neural network that is inspired by the neuroscience concept of predictive coding (Rao and Ballard, 1999; Friston, 2005).'
+    pypi_badge:                'no'
+    pypi_disable_upload:       'no'
+    release_date:              '8 July 2016'
+    repo_hosting:              'github.com'
+    repo_hosting_domain:       'github.com'
+    repo_name:                 'prednet'
+    repo_username:             'coxlab'
+    requiresio:                'no'
+    scrutinizer:               'no'
+    setup_py_uses_setuptools_scm: 'yes'
+    setup_py_uses_test_runner: 'yes'
+    sphinx_docs:               'yes'
+    sphinx_docs_hosting:       'https://coxlab.github.io/prednet/'
+    sphinx_doctest:            'yes'
+    sphinx_theme:              'sphinx-rtd-theme'
+    test_matrix_configurator:  'no'
+    test_matrix_separate_coverage: 'no'
+    test_runner:               'pytest'
+    travis:                    'yes'
+    travis_osx:                'no'
+    version:                   '0.0.0'
+    website:                   'http://www.coxlab.org/'
+    year_from:                 '2016'
+    year_to:                   '2019'

.coveragerc

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+[paths]
+source =
+   src
+   */site-packages
+
+[run]
+branch = true
+source =
+    prednet
+    tests
+parallel = true
+
+[report]
+show_missing = true
+precision = 2
+omit = *migrations*

.editorconfig

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+# see http://editorconfig.org
+root = true
+
+[*]
+end_of_line = lf
+trim_trailing_whitespace = true
+insert_final_newline = true
+indent_style = space
+indent_size = 4
+charset = utf-8
+
+[*.{bat,cmd,ps1}]
+end_of_line = crlf

.gitlab-ci.yml

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+image: ufoym/deepo
+
+default:
+  before_script:
+    - right_after_pull_docker_image=$(date +%s)
+    - echo $(whoami)
+    - echo $USER
+
+    # If we need to apk add openssh-client, then we will need HTTPS_PROXY set first.
+    # This potentially leads to a problem if we need SSH to access the ETC_ENVIRONMENT_LOCATION.
+    # The ETC_ENVIRONMENT_LOCATION is not generally intended for secret keys like the SSH_PRIVATE_KEY.
+    - if [ -z ${ETC_ENVIRONMENT_LOCATION+ABC} ]; then echo "ETC_ENVIRONMENT_LOCATION is unset, so assuming you do not need environment variables set.";
+      else
+    # All of this will be skipped unless you set ETC_ENVIRONMENT_LOCATION in GitLab.
+    # Strictly speaking, this serves the same function as .profile, being run before everything else.
+    # You *could* put arbitrary shell commands in the file, but the intended purpose is
+    # to save on manual work by allowing you to set only one GitLab variable that points
+    # to more variables to set.
+    # Special note if the environment file is used to set up a proxy with HTTPS_PROXY...
+    # $ETC_ENVIRONMENT_LOCATION must be a location that we can access *before* setting up the proxy variables.
+    - echo $ETC_ENVIRONMENT_LOCATION
+    # We do not want the script to hang waiting for a password if the private key is rejected.
+    - mkdir --parents ~/.ssh
+    - echo "PasswordAuthentication=no" >> ~/.ssh/config
+    - echo $SSH_PRIVATE_KEY > SSH.PRIVATE.KEY # If SSH_PRIVATE_KEY is unset, this will just be empty.
+    - wget $ETC_ENVIRONMENT_LOCATION --output-document environment.sh --no-clobber || scp -i SSH.PRIVATE.KEY $ETC_ENVIRONMENT_LOCATION environment.sh
+    - rm SSH.PRIVATE.KEY
+    - cat environment.sh
+    - set -o allexport
+    - source environment.sh
+    - set +o allexport
+    - fi
+
+    - if [ -z ${SSH_PRIVATE_KEY+ABC} ]; then echo "SSH_PRIVATE_KEY is unset, so assuming you do not need SSH set up.";
+      else
+    # All of this will be skipped unless you set SSH_PRIVATE_KEY as a variable
+    - if [ ${#SSH_PRIVATE_KEY} -le 5 ]; then echo "SSH_PRIVATE_KEY looks far too short, something is wrong"; fi
+    - apk add openssh-client || apt-get install --assume-yes openssh-client
+    - echo "adding openssh-client took $(( $(date +%s) - right_after_pull_docker_image)) seconds"
+
+    # ssh-agent -s starts the ssh-agent and then outputs shell commands to run.
+    - eval $(ssh-agent -s)
+
+    ##
+    ## Add the SSH key stored in SSH_PRIVATE_KEY variable to the agent store.
+    ## We're using tr to fix line endings which makes ed25519 keys work
+    ## without extra base64 encoding.
+    ## We use -d because the version of tr on alpine does not recognize --delete.
+    ## https://gitlab.com/gitlab-examples/ssh-private-key/issues/1#note_48526556
+    ##
+    - echo "$SSH_PRIVATE_KEY" | tr -d '\r' | ssh-add -
+
+    ##
+    ## Sometimes we may want to install directly from a git repository.
+    ## Using up-to-the-minute updates of dependencies in our own tests alerts
+    ## us if something breaks with the latest version of a dependency, even if
+    ## that dependency has not made a new release yet.
+    ## In order to pip install directly from git repositories,
+    ## we need to whitelist the public keys of the git servers.
+    ## You may want to add more lines for the domains of any other git servers
+    ## you want to install dependencies from (which may or may not include the
+    ## server that hosts your own repo).
+    ## Similarly, if you want to push to a secondary repo as part of your build
+    ## (as how cookiecutter-pylibrary builds examples and
+    ## pushes to python-nameless), ssh will need to be allowed to reach that
+    ## server.
+    ## https://docs.travis-ci.com/user/ssh-known-hosts/
+    ## https://discuss.circleci.com/t/add-known-hosts-on-startup-via-config-yml-configuration/12022/2
+    ## Unfortunately, there seems to be no way to use ssh-keyscan on a server
+    ## that you can only reach through a proxy. Thus, a simple
+    ## ssh-keyscan -t rsa github.com gitlab.com >> ~/.ssh/known_hosts
+    ## will fail. As a workaround, I just grabbed their public keys now and
+    ## included them. These might go stale eventually, I'm not sure.
+    ##
+    - mkdir --parents ~/.ssh
+    - echo "# github.com:22 SSH-2.0-babeld-f345ed5d\n" >> ~/.ssh/known_hosts
+    - echo "github.com ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAQEAq2A7hRGmdnm9tUDbO9IDSwBK6TbQa+PXYPCPy6rbTrTtw7PHkccKrpp0yVhp5HdEIcKr6pLlVDBfOLX9QUsyCOV0wzfjIJNlGEYsdlLJizHhbn2mUjvSAHQqZETYP81eFzLQNnPHt4EVVUh7VfDESU84KezmD5QlWpXLmvU31/yMf+Se8xhHTvKSCZIFImWwoG6mbUoWf9nzpIoaSjB+weqqUUmpaaasXVal72J+UX2B+2RPW3RcT0eOzQgqlJL3RKrTJvdsjE3JEAvGq3lGHSZXy28G3skua2SmVi/w4yCE6gbODqnTWlg7+wC604ydGXA8VJiS5ap43JXiUFFAaQ==\n" >> ~/.ssh/known_hosts
+    - echo "# gitlab.com:22 SSH-2.0-OpenSSH_7.2p2 Ubuntu-4ubuntu2.8\n" >> ~/.ssh/known_hosts
+    - echo "gitlab.com ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQCsj2bNKTBSpIYDEGk9KxsGh3mySTRgMtXL583qmBpzeQ+jqCMRgBqB98u3z++J1sKlXHWfM9dyhSevkMwSbhoR8XIq/U0tCNyokEi/ueaBMCvbcTHhO7FcwzY92WK4Yt0aGROY5qX2UKSeOvuP4D6TPqKF1onrSzH9bx9XUf2lEdWT/ia1NEKjunUqu1xOB/StKDHMoX4/OKyIzuS0q/T1zOATthvasJFoPrAjkohTyaDUz2LN5JoH839hViyEG82yB+MjcFV5MU3N1l1QL3cVUCh93xSaua1N85qivl+siMkPGbO5xR/En4iEY6K2XPASUEMaieWVNTRCtJ4S8H+9\n" >> ~/.ssh/known_hosts
+    - fi
+
+    # When we get the environment file, it might have some servers for us to whitelist.
+    # Alternatively, maybe there was no ETC_ENVIRONMENT_LOCATION
+    # and SERVERS_TO_WHITELIST_FOR_SSH is just manually set as a GitLab variable.
+    # If SSH_PRIVATE_KEY is not set, then we will silently ignore SERVERS_TO_WHITELIST_FOR_SSH,
+    # since without a key of some kind we cannot use SSH anyway.
+    # This allows us to share around a common ETC_ENVIRONMENT_LOCATION that includes SERVERS_TO_WHITELIST_FOR_SSH,
+    # even though only some people actually use SSH for anything.
+    - if [ -z ${SERVERS_TO_WHITELIST_FOR_SSH+ABC} ] || [ -z ${SSH_PRIVATE_KEY+ABC} ]; then echo "SERVERS_TO_WHITELIST_FOR_SSH and SSH_PRIVATE_KEY are not both set, so assuming you do not need any servers whitelisted for SSH.";
+      else
+    - echo $SERVERS_TO_WHITELIST_FOR_SSH
+    - mkdir --parents ~/.ssh
+    - ssh-keyscan -t rsa $SERVERS_TO_WHITELIST_FOR_SSH >> ~/.ssh/known_hosts
+    - fi
+
+    - pip install --upgrade pip
+    - if [ -z ${PROXY_CA_PEM+ABC} ]; then echo "PROXY_CA_PEM is unset, so assuming you do not need a merged CA certificate set up.";
+      else
+    # All of this will be skipped unless you set PROXY_CA_PEM in GitLab.
+    # You will usually want to cat your.pem | xclip and paste it in as a File on GitLab.
+    # See the KUBE_CA_PEM example at https://docs.gitlab.com/ee/ci/variables/README.html#variable-types
+    - right_before_pull_cert=$(date +%s)
+    - if [ ${#PROXY_CA_PEM} -ge 1024 ]; then
+    - echo "The PROXY_CA_PEM filename looks far too long, did you set it as a Variable instead of a File?"
+    # If it's the full certificate rather than a filename, write it to a file and save the file name.
+    - echo "$PROXY_CA_PEM" > tmp-proxy-ca.pem
+    # The quotes are very important here; echo $PROXY_CA_PEM will destroy the
+    # newlines, and requests will (silently!) fail to parse the certificate,
+    # leading to SSLError SSLCertVerificationError 'certificate verify failed self signed certificate in certificate chain (_ssl.c:1076)'
+    - PROXY_CA_PEM=tmp-proxy-ca.pem
+      ; fi
+    # If some of the links in your documentation require a special PEM to verify,
+    # then sphinx -b linkcheck will fail without that PEM.
+    # But setting REQUESTS_CA_BUNDLE to that PEM will cause other links to fail,
+    # because the runner will only accept that PEM, not the defaults.
+    # Therefore you will usually want to bundle all certificates together with
+    # cat `python -c "import requests; print(requests.certs.where())"` ~/your.pem > ~/bundled.pem
+    # pip uses requests, but not the normal requests.
+    # pip uses a vendored version of requests, so that pip will still work if anything goes wrong with your requests installation.
+    # We find where that vendored version of requests keeps its certs and merge in the cert from PROXY_CA_PEM.
+    # On some systems, we might need to try the import twice, and the first time, it will fail with an AttributeError.
+    # Therefore we need a block to suppress the AttributeError, which requires a colon.
+    # But that causes parsing of .gitlab-ci.yml to fail with "before_script config should be an array of strings",
+    # so we need to wrap the entire line in ''.
+    # https://gitlab.com/gitlab-org/gitlab-foss/merge_requests/5481
+    - 'echo -e "import contextlib\nwith contextlib.suppress(AttributeError): import pip._vendor.requests\nfrom pip._vendor.requests.certs import where\nprint(where())" | python'
+    - 'cat `echo -e "import contextlib\nwith contextlib.suppress(AttributeError): import pip._vendor.requests\nfrom pip._vendor.requests.certs import where\nprint(where())" | python` $PROXY_CA_PEM > bundled.pem'
+    - export REQUESTS_CA_BUNDLE=bundled.pem
+    - echo "Merging the certificate bundle took $(( $(date +%s) - right_before_pull_cert)) seconds total"
+    - fi
+
+    ##
+    ## With all our proxy variables and certificates in place, we should now be
+    ## able to install from repositores, and optionally push to repositories.
+    ## Optionally, if you will be making any git commits, set the user name and
+    ## email.
+    ##
+    #- git config --global user.email "[email protected]"
+    #- git config --global user.name "Bill Lotter"
+
+    # With --sitepackages, we can save time by installing once
+    # for both regular tests and documentation checks.
+    - python -c "import enum; print(enum.__file__)"
+    - pip uninstall --yes enum34
+    - pip install .
+
+# In general we want to use tox -e docs, but GitLab.com will not deploy Pages
+# if the pages build fails.
+# The pages build will fail if you use tox -e docs with a link to your GitLab
+# Pages documentation that is not yet deployed, because tox -e docs includes
+# sphinx-build -b linkcheck. So the pages will never get deployed...
+# That's why we deploy pages with no checks here.
+# The tests will still run linkcheck on the documentation.
+# Since "It may take up to 30 minutes before the site is available after the
+# first deployment." (per GitLab), the tests will still fail for a little
+# while.
+pages:
+  tags:
+  - docker
+  stage: build
+  # On GitLab, the stages are build->test->deploy.
+  # If the test stage fails, the deploy stage is skipped.
+  script:
+  - pip install -r docs/requirements.txt
+  - sphinx-build -E -b html docs dist/docs
+  - mv dist/docs/ public/
+  artifacts:
+    paths:
+    - public
+  only:
+  - master
+
+test:
+  tags:
+  - docker
+  stage: test
+  script:
+  # apk add any needed packages not included in the image.
+  # check-manifest, used in tox -e check, requires git,
+  # so we need to either use an image that includes git or
+  # apk add git here.
+  # If using an image that does not include tox, we will
+  # need to pip install tox here.
+  - pip install tox
+  - git --version
+  - python --version
+  - python2 --version || echo "python2 is not installed."
+  - virtualenv --version
+  - pip --version
+  - tox --version
+  - uname --all
+  - lsb_release --all || echo "lsb_release is not supported on this host."
+  - start_tox=$(date +%s)
+  # When testing locally, we might not want to set sitepackages=true,
+  # because the local machine might have all kinds of weird things in the
+  # environment. But for continuous integration, we do want sitepackages=true,
+  # because it allows us to use a Docker image with some packages already
+  # installed to accelerate testing.
+  - tox --sitepackages
+  - echo "tox tests took $(( $(date +%s) - start_tox)) seconds"
+  - echo "Everything after pulling the Docker image took $(( $(date +%s) - right_after_pull_docker_image)) seconds total"
+