Merge branch 'master' of https://github.com/ejolly/pymer4

Author: ejolly

.travis.yml

@@ -1,9 +1,21 @@
 # requires a valid GIT_TOKEN, ANACONDA_TOKEN, PYPI_TOKEN in TravisCI settings
 env:
-  - PACKAGE_NAME: pymer4   # for the conda_upload.sh deploy script
+  global:
+    - PACKAGE_NAME: pymer4   # for the conda_upload.sh deploy script
 
 language: minimal
 
+jobs:
+  include:
+    - name: "3.6 build"
+      env: PYV=3.6
+    - name: "3.7 build"
+      env: PYV=3.7
+    - name: "3.8 build"
+      env: PYV=3.8
+    - name: "default python build"
+      env: PYV=""
+
 before_install:
   # b.c conda build GIT_BUILD_STR works (or not) in mysterious ways ...
   # pfx g means ordinary commit, r means github tagged vM.N.P release
@@ -19,38 +31,48 @@ before_install:
 
 install:
   - conda install -q conda-build conda-verify
-  - conda build conda -c defaults -c conda-forge
-  - conda create --name pymer4_env pymer4 -c local -c defaults -c conda-forge
-  - conda activate pymer4_env  # run pytests in conda env
+  - conda build --python=${PYV} -c defaults -c conda-forge conda
+
+script:
+  # install and test py 3.x variants
+  - conda create -n pyenv_${PYV} python=${PYV} pymer4 -c local -c defaults -c conda-forge
+  - conda activate pyenv_${PYV}
   - conda install black pytest-cov
   - conda list
   - lscpu
   - python -c 'import numpy; numpy.show_config()'
-
-script:
   - black --check --verbose .
   - pytest --cov=pymer4
 
 after_success:
-  - conda install codecov && codecov
 
 before_deploy:
   # install necessary packages and refresh the docs before deployment
   - conda install sphinx sphinx_bootstrap_theme sphinx-gallery -c conda-forge
   - cd docs && make clean && make html && cd .. && pwd
 
+# Gotcha: deploy on conditions are bash if [[ ... ]]; then deploy ; fi
+# and **NOT** TravisCI condition syntax used for conditional execution
 deploy:
 
+  # moved codecov from after_success
+  - provider: script
+    skip_cleanup: true
+    script: conda install codecov && codecov
+    on:
+      branch: master
+      condition: $PYV == "3.8"
+
   # allow any commit to master or dev to refresh the docs on gh-pages
   - provider: pages
     skip_cleanup: true
     keep-history: false
     github_token: $GITHUB_TOKEN  # from github, set in TravisCI settings
     local_dir: ./docs/_build/html
     on:
-      branch: master
       # all_branches: true  # testing only
-      # condition: $TRAVIS_BRANCH =~ ^(master)$|^(dev)$
+      branch: master
+      condition: $PYV == "3.8"
 
   # this script manages conda package uploads. It routes routine
   # master commits to the pre-release label and manual github releases
@@ -59,7 +81,8 @@ deploy:
     skip_cleanup: true
     script: bash ./ci/conda_upload.sh
     on:
-      all_branches: true  # always dry-run the script
+      condition: $PYV =~ ^3\.[678]$  # python 3.6, 3.7, 3.8 jobs
+      all_branches: true  # dry-run the script on any branch
 
   # only upload manual github releases tagged vM.N.P to PyPI
   # so M.N.P on Anaconda Cloud channel/label/main == PyPI
@@ -70,5 +93,4 @@ deploy:
     on:
       branch: master
       tags: true
-      condition: $TRAVIS_TAG =~ ^v[0-9]+\.[0-9]+\.[0-9]+$
-
+      condition: $TRAVIS_TAG =~ ^v[0-9]+\.[0-9]+\.[0-9]+$ && $PYV == "3.8"

ci/conda_upload.sh

@@ -1,7 +1,8 @@
 # Anaconda Cloud package uploader.
 # 
-#  * This assumes TravisCI ran conda build and the linux-64 package tar.bz
-#    is in the default location /home/travis/miniconda3/conda-bld/linux-64
+#  * This assumes TravisCI ran conda build python=$PYV conda 
+#    and the one linux-64 tarball is in the default location
+#    /home/travis/miniconda3/conda-bld/linux-64
 # 
 #  * The upload only fires if the package version from meta.yaml is
 #    (exactly) Major.Minor.Patch and $TRAVIS_BRANCH is master or
@@ -21,6 +22,9 @@ if [[ -z ${CONDA_DEFAULT_ENV} ]]; then
 fi
 
 # intended for TravisCI deploy but can be tricked into running locally
+echo PACKAGE_NAME=$PACKAGE_NAME
+echo TRAVIS=$TRAVIS
+echo TRAVIS_BRANCH=$TRAVIS_BRANCH
 if [[ "$TRAVIS" != "true" || -z "$TRAVIS_BRANCH" || -z "${PACKAGE_NAME}" ]]; then
     echo "conda_upload.sh is meant to run on TravisCI"
     exit -2
@@ -30,8 +34,8 @@ fi
 # bld_prefix=${HOME}/miniconda3
 bld_prefix="/home/travis/miniconda"  # from the .travis.yml
 
-# on travis there should be a single linux-64 package tarball. insist
-tarball=`/bin/ls -1 ${bld_prefix}/conda-bld/linux-64/${PACKAGE_NAME}-*-*.tar.bz2`
+# for travis parallel jobs there should be 1 py3X linux-64 tarball, insist
+tarball=`/bin/ls -1ta ${bld_prefix}/conda-bld/linux-64/${PACKAGE_NAME}-*-*.tar.bz2`
 n_tarballs=`echo "${tarball}" | wc -w`
 if (( $n_tarballs != 1 )); then
     echo "found $n_tarballs package tarballs there must be exactly 1"
@@ -55,7 +59,7 @@ mmp=$(echo $version | sed -n "s/\(\([0-9]\+\.\)\{1,2\}[0-9]\+\).*/\1/p")
 # assume this is a dry run, unless version is M.N.P or M.N.P.devXXX and
 # TRAVIS_BRANCH is master or a tagged vM.N.P release, in which case,
 # set the destination label appropriately.
-label="dry-run"  
+label="dry-run"
 if [[ "${version}" =~ ^${mmp}(.dev[0-9]+){0,1}$ ]]; then
 
     # commit to master uploads to pre-release
@@ -74,11 +78,11 @@ fi
 mkdir -p ${bld_prefix}/conda-convert/linux-64
 cp ${tarball} ${bld_prefix}/conda-convert/linux-64
 cd ${bld_prefix}/conda-convert
-conda convert -p linux-64 -p osx-64 -p win-64  linux-64/${PACKAGE_NAME}*tar.bz2
+conda convert -p linux-64 -p osx-64 -p win-64  linux-64/${PACKAGE_NAME}-*-*.tar.bz2
 
 # POSIX trick sets $ANACONDA_TOKEN if unset or empty string 
 ANACONDA_TOKEN=${ANACONDA_TOKEN:-[not_set]}
-conda_cmd="anaconda --token $ANACONDA_TOKEN upload ./**/${PACKAGE_NAME}*.tar.bz2 --label ${label} --skip-existing"
+conda_cmd="anaconda --token $ANACONDA_TOKEN upload ./**/${PACKAGE_NAME}*-*.tar.bz2 --label ${label} --skip-existing"
 
 # echo values to the TravisCI log for general info/debugging
 echo "package name: $PACKAGE_NAME"
@@ -91,7 +95,7 @@ echo "tarball: $tarball"
 echo "conda label: ${label}"
 echo "conda upload command: ${conda_cmd}"
 echo "platforms:"
-echo "$(ls ./**/${PACKAGE_NAME}*.tar.bz2)"
+echo "$(ls ./**/${PACKAGE_NAME}-*-*.tar.bz2)"
 
 # trigger the upload and destination or 
 if [[ $ANACONDA_TOKEN != "[not_set]" && ( $label = "main" || $label = "pre-release" ) ]]; then

conda/meta.yaml

@@ -13,25 +13,26 @@ build:
     # script: python setup.py install --single-version-externally-managed --record=record.txt
     script: pip install . -vv --no-deps
     # abandoned conda build GIT_BUILD_STRING env variable
-    string: {{ environ.get("GIT_ABBREV_COMMIT", "no_git_abbrev_commit") }}_{{ environ.get("PKG_BUILDNUM", "no_pkg_buildnum") }}
+    string: py{{environ.get("CONDA_PY", "XX")}}{{environ.get("GIT_ABBREV_COMMIT", "no_git_abbrev_commit") }}_{{ environ.get("PKG_BUILDNUM", "no_pkg_buildnum") }}
 
 requirements:
 
   host:
-    - python  # else test section fails during TravisCI conda build
+    # else test section fails during TravisCI conda build
+    - python {{ python }}
     - pip
 
   run:
-    - python >=3.6
+    - python {{ python }}
     - deepdish >=0.3.6
     - joblib >=0.14
     - matplotlib >=3.0
     - numpy >=1.16
     - pandas >=1.0
-    - patsy =>0.5.1
+    - patsy >=0.5.1
     - rpy2 >=3.3.2
-    - scipy>=1.4.0
-    - seaborn>=0.10.0
+    - scipy >=1.4.0
+    - seaborn >=0.10.0
     - r-base
     - r-lme4
     - r-lmerTest