Merge pull request #109 from czbiohub/joss-review-redux

JOSS review comments -- redux
czbiohub-sf · Aug 26, 2020 · f6cdff4 · f6cdff4
2 parents f9085c9 + dbae4da
commit f6cdff4
Show file tree

Hide file tree

Showing 20 changed files with 366 additions and 275 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -23,117 +23,117 @@ matrix:
         - pip3 install -r test_requirements.txt
         - pip3 install .
 
-    # - os: linux
-    #   python: "3.8-dev"
-    #   install:
-    #     - pip3 install -r requirements.txt 
-    #     - pip3 install -r test_requirements.txt
-    #     - pip3 install .
+    - os: linux
+      python: "3.8-dev"
+      install:
+        - pip3 install -r requirements.txt 
+        - pip3 install -r test_requirements.txt
+        - pip3 install .
 
-    # - os: linux
-    #   python: "3.9-dev"
-    #   install:
-    #     - pip3 install -r requirements.txt 
-    #     - pip3 install -r test_requirements.txt
-    #     - pip3 install .
+    - os: linux
+      python: "3.9-dev"
+      install:
+        - pip3 install -r requirements.txt 
+        - pip3 install -r test_requirements.txt
+        - pip3 install .
 
-    # - os: linux
-    #   python: "pypy3"
-    #   install:
-    #     - pip3 install -r requirements.txt 
-    #     - pip3 install -r test_requirements.txt
-    #     - pip3 install .
+    - os: linux
+      python: "pypy3"
+      install:
+        - pip3 install -r requirements.txt 
+        - pip3 install -r test_requirements.txt
+        - pip3 install .
 
-    # - name: "Python 3.6.6 OSX"
-    #   os: osx
-    #   language: generic
-    #   env: PYTHON=3.6.6'
-    #   before_install:
-    #     - brew update
-    #     - brew install openssl
-    #     - brew install zlib
-    #     - brew outdated pyenv || brew upgrade pyenv
-    #     - brew install pyenv-virtualenv
-    #     - pyenv install 3.6.6
-    #     - export PYENV_VERSION=3.6.6
-    #     - export PATH="/Users/travis/.pyenv/shims:${PATH}"
-    #     - pyenv virtualenv venv
-    #     - source /Users/travis/.pyenv/versions/venv/bin/activate
-    #     - python --version
-    #   install:
-    #     - python -m pip install -U pip
-    #     - sudo pip install setuptools
-    #     - sudo pip install -r requirements.txt -e .
-    #     - sudo pip install -r test_requirements.txt -e .
+    - name: "Python 3.6.6 OSX"
+      os: osx
+      language: generic
+      env: PYTHON=3.6.6'
+      before_install:
+        - brew update
+        - brew install openssl
+        - brew install zlib
+        - brew outdated pyenv || brew upgrade pyenv
+        - brew install pyenv-virtualenv
+        - pyenv install 3.6.6
+        - export PYENV_VERSION=3.6.6
+        - export PATH="/Users/travis/.pyenv/shims:${PATH}"
+        - pyenv virtualenv venv
+        - source /Users/travis/.pyenv/versions/venv/bin/activate
+        - python --version
+      install:
+        - python -m pip install -U pip
+        - sudo pip install setuptools
+        - sudo pip install -r requirements.txt -e .
+        - sudo pip install -r test_requirements.txt -e .
 
-    # - name: "Python 3.7.7 OSX"
-    #   os: osx
-    #   language: generic
-    #   env: PYTHON=3.7.7'
-    #   before_install:
-    #     - brew update
-    #     - brew install openssl
-    #     - brew install zlib
-    #     - brew outdated pyenv || brew upgrade pyenv
-    #     - brew install pyenv-virtualenv
-    #     - pyenv install 3.7.7
-    #     - export PYENV_VERSION=3.7.7
-    #     - export PATH="/Users/travis/.pyenv/shims:${PATH}"
-    #     - pyenv virtualenv venv
-    #     - source /Users/travis/.pyenv/versions/venv/bin/activate
-    #     - python --version
-    #   install:
-    #     - python -m pip install -U pip
-    #     - sudo pip install setuptools
-    #     - sudo pip install -r requirements.txt -e .
-    #     - sudo pip install -r test_requirements.txt -e .
+    - name: "Python 3.7.7 OSX"
+      os: osx
+      language: generic
+      env: PYTHON=3.7.7'
+      before_install:
+        - brew update
+        - brew install openssl
+        - brew install zlib
+        - brew outdated pyenv || brew upgrade pyenv
+        - brew install pyenv-virtualenv
+        - pyenv install 3.7.7
+        - export PYENV_VERSION=3.7.7
+        - export PATH="/Users/travis/.pyenv/shims:${PATH}"
+        - pyenv virtualenv venv
+        - source /Users/travis/.pyenv/versions/venv/bin/activate
+        - python --version
+      install:
+        - python -m pip install -U pip
+        - sudo pip install setuptools
+        - sudo pip install -r requirements.txt -e .
+        - sudo pip install -r test_requirements.txt -e .
 
-    # - name: "Python 3.8.2 OSX"
-    #   os: osx
-    #   language: generic
-    #   env: PYTHON=3.8.2'
-    #   before_install:
-    #     - brew update
-    #     - brew install openssl
-    #     - brew install zlib
-    #     - brew outdated pyenv || brew upgrade pyenv
-    #     - brew install pyenv-virtualenv
-    #     - pyenv install 3.8.2
-    #     - export PYENV_VERSION=3.8.2
-    #     - export PATH="/Users/travis/.pyenv/shims:${PATH}"
-    #     - pyenv virtualenv venv
-    #     - source /Users/travis/.pyenv/versions/venv/bin/activate
-    #     - python --version
-    #   install:
-    #     - python -m pip install -U pip
-    #     - sudo pip install setuptools
-    #     - sudo pip install -r requirements.txt -e .
-    #     - sudo pip install -r test_requirements.txt -e .
+    - name: "Python 3.8.2 OSX"
+      os: osx
+      language: generic
+      env: PYTHON=3.8.2'
+      before_install:
+        - brew update
+        - brew install openssl
+        - brew install zlib
+        - brew outdated pyenv || brew upgrade pyenv
+        - brew install pyenv-virtualenv
+        - pyenv install 3.8.2
+        - export PYENV_VERSION=3.8.2
+        - export PATH="/Users/travis/.pyenv/shims:${PATH}"
+        - pyenv virtualenv venv
+        - source /Users/travis/.pyenv/versions/venv/bin/activate
+        - python --version
+      install:
+        - python -m pip install -U pip
+        - sudo pip install setuptools
+        - sudo pip install -r requirements.txt -e .
+        - sudo pip install -r test_requirements.txt -e .
 
-    # - name: "Python 3.8.0 Windows"
-    #   os: windows                 
-    #   language: shell       
-    #   before_install:
-    #     - choco install python --version 3.8.0
-    #     - python -m pip install --upgrade pip
-    #   env: PATH=/c/Python38:/c/Python38/Scripts:$PATH
-    #   install:
-    #     - python -m pip install -U pip # maybe dont need this
-    #     - pip install setuptools
-    #     - pip install -r requirements.txt -e .
-    #     - pip install -r test_requirements.txt -e .
+    - name: "Python 3.8.0 Windows"
+      os: windows                 
+      language: shell       
+      before_install:
+        - choco install python --version 3.8.0
+        - python -m pip install --upgrade pip
+      env: PATH=/c/Python38:/c/Python38/Scripts:$PATH
+      install:
+        - python -m pip install -U pip # maybe dont need this
+        - pip install setuptools
+        - pip install -r requirements.txt -e .
+        - pip install -r test_requirements.txt -e .
 
-  # allow_failures:
-  #   - python: "3.8-dev"
-  #   - python: "3.9-dev"
-  #   - python: "pypy3"
-  #   - os: windows
+  allow_failures:
+    - python: "3.8-dev"
+    - python: "3.9-dev"
+    - python: "pypy3"
+    - os: windows
 
 script:
     - make test
-    - make coverage
-    - make lint
+#    - make coverage
+#    - make lint
 
-after_script:
-    - pip3 install codecov
-    - codecov
+#after_script:
+#    - pip3 install codecov
+#    - codecov
diff --git a/Makefile b/Makefile
@@ -16,4 +16,4 @@ lint:
 
 install:
 	pip install -r requirements.txt
-	pip install -e .
+	pip install .