Merge branch 'release/0.99.9'

viscid-hub · Aug 20, 2018 · dd921a6 · dd921a6
2 parents 62ce8c6 + 4ebeff1
commit dd921a6
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diff --git a/.travis.yml b/.travis.yml
@@ -34,27 +34,29 @@ before_install:
 
   # before we build, check to see if we're in a release branch, and if
   # so, then do some 0th order validation on the viscid.__version__
-  - 'if [[ ($TRAVIS_BRANCH =~ ^(.*release.*|master)$) ]]; then
-       if [ "$(grep -E "__version__\s*=" viscid/__init__.py | grep -E "(dev|travis)")" != "" ]; then
-         echo "Oops, you are preparing a release, but you still have either";
-         echo "dev or travis in the version number";
-         false;
-       fi
-     elif [[ $TRAVIS_BRANCH =~ ${deployable} ]]; then
-       if [ "$(grep -E "__version__\s*=" viscid/__init__.py | grep ${TRAVIS_BRANCH} )" == "" ]; then
-         echo "Oops, You are on a deployable branch (that is not master), ";
-         echo "but the branch name is not in the version number";
-         false;
-       fi
-     fi'
+  - |
+    if [[ ($TRAVIS_BRANCH =~ ^(.*release.*|master)$) ]]; then
+      if [ "$(grep -E "__version__\s*=" viscid/__init__.py | grep -E "(dev|travis)")" != "" ]; then
+        echo "Oops, you are preparing a release, but you still have either"
+        echo "dev or travis in the version number"
+        false
+      fi
+    elif [[ $TRAVIS_BRANCH =~ ${deployable} ]]; then
+      if [ "$(grep -E "__version__\s*=" viscid/__init__.py | grep ${TRAVIS_BRANCH} )" == "" ]; then
+        echo "Oops, You are on a deployable branch (that is not master), "
+        echo "but the branch name is not in the version number"
+        false
+      fi
+    fi
 
   # make sure the version string appears in CHANGES.md
-  - 'ver_re="__version__.*[\"'']+([^\"'']+)[\"'']+"'
-  - 'version=$([[ "$(grep -E "__version__\s*=" viscid/__init__.py)" =~ ${ver_re} ]]; echo "${BASH_REMATCH[1]}")'
-  - 'if [ "$(grep -E "${version}\s*$" CHANGES.md)" == "" ]; then
-       echo "Oops, the version ${version} does not appear in CHANGES.md";
-       false;
-     fi'
+  - |
+    ver_re="__version__.*[\"'']+([^\"'']+)[\"'']+"
+    version=$([[ "$(grep -E "__version__\s*=" viscid/__init__.py)" =~ ${ver_re} ]]; echo "${BASH_REMATCH[1]}")
+    if [ "$(grep -E "${version}\s*$" CHANGES.md)" == "" ]; then
+      echo "Oops, the version ${version} does not appear in CHANGES.md"
+      false
+    fi
 
   # setup deployment key
   # make the encrypted archives with the following...
@@ -84,56 +86,66 @@ before_install:
   # then...
   # Add the public key to the github project ${HG_USER}/Viscid-docs
   # as a "Deploy key" with write access
-  - 'mkdir -p ${HOME}/.ssh'
-  - 'chmod 700 ${HOME}/.ssh'
-  - 'if [ "${TRAVIS_REPO_SLUG}" == "viscid-hub/Viscid" ]; then
-       openssl aes-256-cbc -K $encrypted_0b3ef9041727_key -iv $encrypted_0b3ef9041727_iv -in resources/.archive.viscid-hub.tar.gz.enc -out ./.archive.tar.gz -d;
-       export DEPLOY_SLUG="${TRAVIS_REPO_SLUG}-docs";
-       export DEPLOY_DOCS="true";
-       export DEPLOY_TESTS="true";
-     elif [ "${TRAVIS_REPO_SLUG}" == "KristoforMaynard/Viscid" ]; then
-       openssl aes-256-cbc -K $encrypted_0b3ef9041727_key -iv $encrypted_0b3ef9041727_iv -in resources/.archive.KristoforMaynard.tar.gz.enc -out ./.archive.tar.gz -d;
-       export DEPLOY_SLUG="${TRAVIS_REPO_SLUG}-docs";
-       export DEPLOY_DOCS="false";
-       export DEPLOY_TESTS="true";
-     else
-       export DEPLOY_SLUG="";
-       export DEPLOY_DOCS="false";
-       export DEPLOY_TESTS="false";
-     fi'
-  - 'if [ -f ./.archive.tar.gz ]; then
-       mkdir .archive;
-       tar -xf .archive.tar.gz -C .archive;
-       mkdir -p ${HOME}/.ssh;
-       chmod 700 ${HOME}/.ssh;
-       mv .archive/id_rsa ${HOME}/.ssh/id_rsa;
-       chmod 600 ${HOME}/.ssh/id_rsa;
-     fi'
-  - 'echo "Deployment info: DEPLOY_SLUG: ${DEPLOY_SLUG}";
-     echo "Deployment info: DEPLOY_DOCS: ${DEPLOY_DOCS}";
-     echo "Deployment info: DEPLOY_TESTS: ${DEPLOY_TESTS}";
-     ls -la ${HOME}/.ssh;'
+  - |
+    mkdir -p ${HOME}/.ssh
+    chmod 700 ${HOME}/.ssh
+
+  - |
+    if [ "${TRAVIS_REPO_SLUG}" == "viscid-hub/Viscid" ]; then
+      openssl aes-256-cbc -K $encrypted_0b3ef9041727_key -iv $encrypted_0b3ef9041727_iv -in resources/.archive.viscid-hub.tar.gz.enc -out ./.archive.tar.gz -d
+      export DEPLOY_SLUG="${TRAVIS_REPO_SLUG}-docs"
+      export DEPLOY_DOCS="true"
+      export DEPLOY_TESTS="true"
+    elif [ "${TRAVIS_REPO_SLUG}" == "KristoforMaynard/Viscid" ]; then
+      openssl aes-256-cbc -K $encrypted_0b3ef9041727_key -iv $encrypted_0b3ef9041727_iv -in resources/.archive.KristoforMaynard.tar.gz.enc -out ./.archive.tar.gz -d
+      export DEPLOY_SLUG="${TRAVIS_REPO_SLUG}-docs"
+      export DEPLOY_DOCS="false"
+      export DEPLOY_TESTS="true"
+    else
+      export DEPLOY_SLUG=""
+      export DEPLOY_DOCS="false"
+      export DEPLOY_TESTS="false"
+    fi
+
+  - |
+    if [ -f ./.archive.tar.gz ]; then
+      mkdir .archive
+      tar -xf .archive.tar.gz -C .archive
+      mkdir -p ${HOME}/.ssh
+      chmod 700 ${HOME}/.ssh
+      mv .archive/id_rsa ${HOME}/.ssh/id_rsa
+      chmod 600 ${HOME}/.ssh/id_rsa
+    fi
+
+  - |
+    echo "Deployment info: DEPLOY_SLUG: ${DEPLOY_SLUG}"
+    echo "Deployment info: DEPLOY_DOCS: ${DEPLOY_DOCS}"
+    echo "Deployment info: DEPLOY_TESTS: ${DEPLOY_TESTS}"
+    ls -la ${HOME}/.ssh
 
   ## Now setup the Anaconda tools
   # it saves some download time to use the same python iff 2.7
-  - 'if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
-       export CONDA_URL="https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh";
-     else
-       export CONDA_URL="https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh";
-     fi'
+  - |
+    if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
+      export CONDA_URL="https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh"
+    else
+      export CONDA_URL="https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh"
+    fi
+
   # linux has wget, OS X has curl... such is life
-  - 'if [[ "$(which wget &>/dev/null && echo $?)" == "0" ]]; then
-       wget "${CONDA_URL}" -O miniconda.sh;
-     else
-       curl "${CONDA_URL}" > miniconda.sh;
-     fi'
-  - bash miniconda.sh -b -p $HOME/miniconda
-  - export PATH="$HOME/miniconda/bin:$PATH"
-  - hash -r
-  - conda config --set always_yes yes --set changeps1 no
-  # updating conda always causes weird bugs
-  # - conda update -q conda
-  # Useful for debugging any issues with conda
+  - |
+    if [[ "$(which wget &>/dev/null && echo $?)" == "0" ]]; then
+      wget "${CONDA_URL}" -O miniconda.sh
+    else
+      curl "${CONDA_URL}" > miniconda.sh
+    fi
+
+  - |
+    bash miniconda.sh -b -p $HOME/miniconda
+    export PATH="$HOME/miniconda/bin:$PATH"
+    hash -r
+    conda config --set always_yes yes --set changeps1 no
+
   - conda info -a
 
   ## Now setup some Viscid specific things, like rc files and make sure
@@ -158,52 +170,58 @@ install:
 
   # if conda package list doesn't match the cached one, just blast
   # the cached conda environment
-  - 'if [ -f ${cached_env_spec} ]; then
-       if [ "$(diff -qw ${env_spec} ${cached_env_spec})" != "" ]; then
-         echo "Package Lists Differed, killing current venv";
-         echo "$(diff -w ${env_spec} ${cached_env_spec})";
-         rm ${cached_env_spec};
-         rm -rf ${envpath};
-       fi
-     fi'
+  - |
+    if [ -f ${cached_env_spec} ]; then
+      if [ "$(diff -qw ${env_spec} ${cached_env_spec})" != "" ]; then
+        echo "Package Lists Differed, killing current venv";
+        echo "$(diff -w ${env_spec} ${cached_env_spec})";
+        rm ${cached_env_spec};
+        rm -rf ${envpath};
+      fi
+    fi
 
   # if the conda envronment we need isn't cached, create it, otherwise
   # do an update
-  - 'if [ ! -d "${envpath}" ]; then
-       conda env create -qf ${env_spec};
-       source activate ${env_name};
-       cp ${env_spec} ${cached_env_spec};
-     else
-       source activate ${env_name};
-       conda update --all --yes;
-     fi'
+  - |
+    if [ ! -d "${envpath}" ]; then
+      conda env create -qf ${env_spec};
+      source activate ${env_name};
+      cp ${env_spec} ${cached_env_spec};
+    else
+      source activate ${env_name};
+      conda update --all --yes;
+    fi
 
   # if deplying docs, run tests inplace, this makes preparing the docs
   # faster since cython's fused types makes 8 times too much code, ug!
-  - 'if [ "${PREPARE_DOCS}" == "1" ]; then
-       make inplace;
-       export PATH="${PWD}/scripts:${PATH}";
-       export PYTHONPATH="${PWD}:${PYTHONPATH}";
-     else
-       rm -rf ${prefix};
-       export PATH="${prefix}/bin:${PATH}";
-       export PYTHONPATH="${prefix}:${PYTHONPATH}";
-       mkdir -p "${prefix}";
-       python setup.py install --prefix=${prefix} --install-lib=${prefix};
-     fi'
+  - |
+    if [ "${PREPARE_DOCS}" == "1" ]; then
+      make inplace;
+      export PATH="${PWD}/scripts:${PATH}";
+      export PYTHONPATH="${PWD}:${PYTHONPATH}";
+    else
+      rm -rf ${prefix};
+      export PATH="${prefix}/bin:${PATH}";
+      export PYTHONPATH="${prefix}:${PYTHONPATH}";
+      mkdir -p "${prefix}";
+      python setup.py install --prefix=${prefix} --install-lib=${prefix};
+    fi
 
 before_script:
   - 'if [ "${FLAKE}" == "1" ]; then make flake8; fi'
 
 script:
-  - 'if [ "${PREPARE_DOCS}" == "1" ]; then
-       make check;
-     else
-       make instcheck;
-     fi'
-  - 'if [[ $TRAVIS_BRANCH =~ ${deployable}$ && "${DEPLOY_TESTS}" == "true" ]]; then
-       make deploy-summary;
-     fi'
+  - |
+    if [ "${PREPARE_DOCS}" == "1" ]; then
+      make check;
+    else
+      make instcheck;
+    fi
+
+  - |
+    if [[ $TRAVIS_BRANCH =~ ${deployable}$ && "${DEPLOY_TESTS}" == "true" ]]; then
+      make deploy-summary;
+    fi
 
 deploy:
   provider: "script"

diff --git a/CHANGES.md b/CHANGES.md
@@ -1,6 +1,16 @@
 Changes
 -------
 
+0.99.9
+======
+
+  - add `viscid.mfield` that mimics `numpy.mgrid`
+  - slice-by-value should now be done with imaginary numbers instead of strings encoded like '0.0f'. The string-'f' format will continue to be supported, but imaginary numbers are cleaner for this purpose.
+  - slice-by-array and slice-by-mask (bool array) are now allowed
+  - indexing rules got their own page in the docs
+  - add `viscid.rotation` module for rotation matrix <-> euler angle <-> quaternion conversions
+  - add `viscid.to_dataframe` and `viscid.from_dataframe` to go between datasets and Pandas DataFrame objects
+
 0.99.8
 ======
 

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,4 +1,4 @@
 include viscid/calculator/*.c
 include viscid/plot/images/*.jpg
 include viscid/plot/styles/*.mplstyle
-include sample/*
+include viscid/sample/*
diff --git a/doc/_bstemplates/layout.html b/doc/_bstemplates/layout.html
@@ -7,8 +7,5 @@
 <link rel="apple-touch-icon-precomposed" href="{{ pathto('_static/Vicon_128.png', 1) }}">
 <meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1">
 <meta name="apple-mobile-web-app-capable" content="yes">
+<link rel="stylesheet" href="{{ pathto('_static/my-css.css', 1) }}" type="text/css" />
 {% endblock %}
-
-{% if not bootswatch_css_custom %}
-  {% set bootswatch_css_custom = ['_static/my-css.css'] %}
-{% endif %}
diff --git a/doc/api/viscid.rotation.rst b/doc/api/viscid.rotation.rst
@@ -0,0 +1,7 @@
+viscid.rotation module
+======================
+
+.. automodule:: viscid.rotation
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/api/viscid.rst b/doc/api/viscid.rst
@@ -33,6 +33,7 @@ Submodules
    viscid.npdatetime
    viscid.parallel
    viscid.pyeval
+   viscid.rotation
    viscid.seed
    viscid.sliceutil
    viscid.tree

diff --git a/doc/functions.rst b/doc/functions.rst
@@ -273,7 +273,7 @@ Function                                         Description
 Mayavi Wrappers
 ~~~~~~~~~~~~~~~
 
-Chances are that you want to use these functions. They let you make most Mayavi objects from Viscid data structures (i.e., Fields and SeedGens). In addition, all of these functions allow you to specify a Matplotlib colormap for the data, and it picks up the default colormaps from Matplotlib's rcParams and viscidrc files. How cool is that?
+Chances are that you want to use these functions. They let you make most Mayavi objects from Viscid data structures (i.e., Fields and SeedGens). In addition, all of these functions allow you to specify a Matplotlib colormap for the data, and it picks up the default colormaps from Matplotlib's rcParams and viscidrc files. How cool is that‽
 
 .. cssclass:: table-striped
 

diff --git a/doc/images/3d_cropped.png b/doc/images/3d_cropped.png
diff --git a/doc/index.rst b/doc/index.rst
@@ -110,6 +110,7 @@ Contents
 
   installation
   philosophy
+  indexing
   tutorial/index
   tips_and_tricks
   functions