Moved all CI stuff out of gitlab yml because it is much cleaner. Added conda...

Moved all CI stuff out of gitlab yml because it is much cleaner. Added conda skeleton stuff for building conda packages. Still some work to do

.ci/build_conda_dist.sh

+#!/usr/bin/env bash
+
+conda update conda
+conda install setuptools conda-build
+cd .conda
+
+# get version and name
+version=`python ../setup.py -V`
+name=`python ../setup.py --name`
+
+# get requirements, and make
+# them conda compatible...
+
+# strip all spaces
+reqs=`cat ../requirements.txt | sed -e 's/ //g'`
+
+# add a space after package name -
+# package names must match a-zA-Z0-9_
+reqs=`echo "$reqs" | sed -e "s/^[a-zA-Z0-9_][a-zA-Z0-9_]*/& /g"`
+
+# remove ==, replace it with a space
+reqs=`echo "$reqs" | sed -e "s/==/ /g"`
+
+# wrap each dep in quotes
+reqs=`echo "$reqs" | sed -e "s/^.*$/'&'/g"`
+
+# add a comma at the end
+reqs=`echo "$reqs" | sed -e "s/$/,/g"`
+
+# remove newlines
+reqs=`echo $reqs`
+
+echo "version: $version"
+echo "name:    $name"
+echo "reqs:    $reqs"
+
+echo "{% set name         = 'name' %}"     >  vars.txt
+echo "{% set version      = '$version' %}" >> vars.txt
+echo "{% set requirements = [$reqs] %}"    >> vars.txt
+cat vars.txt meta.yaml > tempfile
+mv tempfile meta.yaml
+rm vars.txt
+
+conda build fslpy
+
+cd ..

.ci/build_doc.sh

+#!/usr/bin/env /bash
+
+python setup.py doc
+mv doc/html doc/"$CI_COMMIT_REF_NAME"

.ci/build_pypi_dist.sh

+#!/usr/bin/env bash
+
+pip install wheel
+python setup.py sdist
+python setup.py bdist_wheel

.ci/deploy_doc.sh

+#!/usr/bin/env bash
+
+rsync -rv doc/"$CI_COMMIT_REF_NAME" "docdeploy:"

.ci/deploy_pypi.sh

+#!/usr/bin/env BASH
+
+pip install setuptools wheel twine
+twine upload dist/*

.ci/patch_version.sh

+#!/usr/bin/env bash
+
+if [[ "x$CI_COMMIT_TAG" != "x" ]]; then
+  echo "Release detected - patching version - $CI_COMMIT_REF_NAME";
+  python -c "import fsl.version as v; v.patchVersion('fsl/version.py', '$CI_COMMIT_REF_NAME')";
+fi

.ci/setup_ssh.sh

+#!/usr/bin/env /bash
+
+##########################################################
+# The setup_ssh script does the following:
+#
+#  - Sets up key-based SSH login, and
+#    installs the private keys, so
+#    we can connect to servers.
+#
+#  - Configures git, and adds the
+#    upstream repo as a remote
+#
+# (see https://docs.gitlab.com/ce/ci/ssh_keys/README.html)
+#
+# NOTE: It is assumed that non-docker
+#       executors are already configured
+#       (or don't need any configuration).
+##########################################################
+
+if [[ -f /.dockerenv ]]; then
+
+ apt-get update -y                           || yum -y check-update                     || true;
+ apt-get install -y openssh-client rsync git || yum install -y openssh-client rsync git || true;
+
+ eval $(ssh-agent -s);
+ mkdir -p $HOME/.ssh;
+
+ echo "$SSH_PRIVATE_KEY_GIT"          > $HOME/.ssh/id_git;
+ echo "$SSH_PRIVATE_KEY_FSL_DOWNLOAD" > $HOME/.ssh/id_fsl_download;
+
+ if [[ "$CI_PROJECT_PATH" == "$UPSTREAM_PROJECT" ]]; then
+   echo "$SSH_PRIVATE_KEY_DOC_DEPLOY" > $HOME/.ssh/id_doc_deploy;
+ fi;
+
+ chmod go-rwx $HOME/.ssh/id_*;
+
+ ssh-add $HOME/.ssh/id_git;
+ ssh-add $HOME/.ssh/id_fsl_download;
+
+ if [[ "$CI_PROJECT_PATH" == "$UPSTREAM_PROJECT" ]]; then
+   ssh-add $HOME/.ssh/id_doc_deploy;
+ fi
+
+ echo "$SSH_SERVER_HOSTKEYS" > $HOME/.ssh/known_hosts;
+
+ touch $HOME/.ssh/config;
+
+ echo "Host ${UPSTREAM_URL##*@}"                    >> $HOME/.ssh/config;
+ echo "    User ${UPSTREAM_URL%@*}"                 >> $HOME/.ssh/config;
+ echo "    IdentityFile $HOME/.ssh/id_git"          >> $HOME/.ssh/config;
+
+ echo "Host docdeploy"                              >> $HOME/.ssh/config;
+ echo "    HostName ${DOC_HOST##*@}"                >> $HOME/.ssh/config;
+ echo "    User ${DOC_HOST%@*}"                     >> $HOME/.ssh/config;
+ echo "    IdentityFile $HOME/.ssh/id_doc_deploy"   >> $HOME/.ssh/config;
+
+ echo "Host fsldownload"                            >> $HOME/.ssh/config;
+ echo "    HostName ${FSL_HOST##*@}"                >> $HOME/.ssh/config;
+ echo "    User ${FSL_HOST%@*}"                     >> $HOME/.ssh/config;
+ echo "    IdentityFile $HOME/.ssh/id_fsl_download" >> $HOME/.ssh/config;
+
+ echo "Host *"                                      >> $HOME/.ssh/config;
+ echo "    IdentitiesOnly yes"                      >> $HOME/.ssh/config;
+
+ git config --global user.name  "Gitlab CI";
+ git config --global user.email "gitlabci@localhost";
+
+ if [[ `git remote -v` == *"upstream"* ]]; then
+     git remote remove upstream;
+ fi;
+ git remote add upstream "$UPSTREAM_URL:$UPSTREAM_PROJECT";
+fi

.ci/test_template.sh

+#!/usr/bin/env bash
+
+# Install $PY_VERSION, xvfb, and all
+# of the wxpython dependencies.
+apt-get update -y || true
+apt-get install -y software-properties-common python-software-properties xvfb libgtk2.0-0 libnotify4 freeglut3 libsdl1.2debian
+add-apt-repository -y ppa:deadsnakes/ppa
+apt-get update -y || true
+apt-get install -y $PY_VERSION "$PY_VERSION"-dev $PY_PACKAGES
+$PY_VENV test.venv
+source test.venv/bin/activate
+pip install --upgrade pip setuptools
+
+# If running on a fork repository, we merge in the
+# upstream/master branch. This is done so that merge
+# requests from fork to the parent repository will
+# have unit tests run on the merged code, something
+# which gitlab CE does not currently do for us.
+if [[ "$CI_PROJECT_PATH" != "$UPSTREAM_PROJECT" ]]; then
+  git fetch upstream;
+  git merge --no-commit --no-ff upstream/master;
+fi;
+
+$INSTALL_WX
+
+# All other deps can be installed as normal.
+# We install test dependenciesd through pip,
+# because if we let setuptools do it, it
+# will build/install everything from source,
+# rather than using wheels.
+pip install -r requirements.txt
+pip install sphinx sphinx-rtd-theme
+pip install pytest pytest-cov pytest-html pytest-runner mock coverage
+
+# style stage
+if [ "$TEST_STYLE"x != "x" ]; then pip install pylint flake8; fi;
+if [ "$TEST_STYLE"x != "x" ]; then flake8                           fsl || true; fi;
+if [ "$TEST_STYLE"x != "x" ]; then pylint --output-format=colorized fsl || true; fi;
+if [ "$TEST_STYLE"x != "x" ]; then exit 0; fi
+
+# We need the FSL atlases for the atlas
+# tests, and need $FSLDIR to be defined
+export FSLDIR=/fsl/
+mkdir -p $FSLDIR/data/
+rsync -rv "fsldownload:data/atlases/" "$FSLDIR/data/atlases/"
+
+# Finally, run the damned tests.
+
+# We run some tests under xvfb-run
+# because they invoke wx. Sleep in
+# between, otherwise xvfb gets upset.
+xvfb-run python setup.py test --addopts="$TEST_OPTS tests/test_idle.py"
+sleep 5
+xvfb-run python setup.py test --addopts="$TEST_OPTS tests/test_platform.py"
+
+# We run the immv/imcpy tests as the nobody
+# user because some tests expect permission
+# denied errors when looking at files, and
+# root never gets denied. Make everything in
+# this directory writable by anybody (which,
+# unintuitively, includes nobody)
+chmod -R a+w `pwd`
+su -s /bin/bash -c 'source test.venv/bin/activate && python setup.py test --addopts="$TEST_OPTS tests/test_immv_imcp.py"' nobody
+
+# All other tests can be run as normal
+python setup.py test --addopts="$TEST_OPTS --ignore=tests/test_idle.py --ignore=tests/test_platform.py --ignore=tests/test_immv_imcp.py"
+python -m coverage report

.conda/bld.bat

+"%PYTHON%" setup.py install
+if errorlevel 1 exit 1

.conda/build.sh

+$PYTHON setup.py install     # Python command to install the script.

.conda/meta.yaml

+package:
+  name:    '{{ name }}'
+  version: '{{ version }}'
+
+source:
+  path:
+    ../
+
+requirements:
+  build:
+    - python
+    - setuptools
+    {% for r in requirements %}
+    - {{ r }}
+    {% endfor %}
+
+  run:
+    - python
+    {% for r in requirements %}
+    - {{ r }}
+    {% endfor %}

.gitlab-ci.yml

@@ -110,81 +110,9 @@ variables:
     - tags
 
 
-##########################################################
-# The setup_ssh anchor contains a before_script section
-# which does the following:
-#
-#  - Sets up key-based SSH login, and
-#    installs the private keys, so
-#    we can connect to servers.
-#
-#  - Configures git, and adds the
-#    upstream repo as a remote
-#
-# (see https://docs.gitlab.com/ce/ci/ssh_keys/README.html)
-#
-# NOTE: It is assumed that non-docker
-#       executors are already configured
-#       (or don't need any configuration).
-##########################################################
-
-
 .setup_ssh: &setup_ssh
   before_script:
-
-    - if [[ -f /.dockerenv ]]; then
-
-        apt-get update -y                           || yum -y check-update                     || true;
-        apt-get install -y openssh-client rsync git || yum install -y openssh-client rsync git || true;
-
-        eval $(ssh-agent -s);
-        mkdir -p $HOME/.ssh;
-
-        echo "$SSH_PRIVATE_KEY_GIT"          > $HOME/.ssh/id_git;
-        echo "$SSH_PRIVATE_KEY_FSL_DOWNLOAD" > $HOME/.ssh/id_fsl_download;
-
-        if [[ "$CI_PROJECT_PATH" == "$UPSTREAM_PROJECT" ]]; then
-          echo "$SSH_PRIVATE_KEY_DOC_DEPLOY" > $HOME/.ssh/id_doc_deploy;
-        fi;
-
-        chmod go-rwx $HOME/.ssh/id_*;
-
-        ssh-add $HOME/.ssh/id_git;
-        ssh-add $HOME/.ssh/id_fsl_download;
-
-        if [[ "$CI_PROJECT_PATH" == "$UPSTREAM_PROJECT" ]]; then
-          ssh-add $HOME/.ssh/id_doc_deploy;
-        fi
-
-        echo "$SSH_SERVER_HOSTKEYS" > $HOME/.ssh/known_hosts;
-
-        touch $HOME/.ssh/config;
-
-        echo "Host ${UPSTREAM_URL##*@}"                    >> $HOME/.ssh/config;
-        echo "    User ${UPSTREAM_URL%@*}"                 >> $HOME/.ssh/config;
-        echo "    IdentityFile $HOME/.ssh/id_git"          >> $HOME/.ssh/config;
-
-        echo "Host docdeploy"                              >> $HOME/.ssh/config;
-        echo "    HostName ${DOC_HOST##*@}"                >> $HOME/.ssh/config;
-        echo "    User ${DOC_HOST%@*}"                     >> $HOME/.ssh/config;
-        echo "    IdentityFile $HOME/.ssh/id_doc_deploy"   >> $HOME/.ssh/config;
-
-        echo "Host fsldownload"                            >> $HOME/.ssh/config;
-        echo "    HostName ${FSL_HOST##*@}"                >> $HOME/.ssh/config;
-        echo "    User ${FSL_HOST%@*}"                     >> $HOME/.ssh/config;
-        echo "    IdentityFile $HOME/.ssh/id_fsl_download" >> $HOME/.ssh/config;
-
-        echo "Host *"                                      >> $HOME/.ssh/config;
-        echo "    IdentitiesOnly yes"                      >> $HOME/.ssh/config;
-
-        git config --global user.name  "Gitlab CI";
-        git config --global user.email "gitlabci@localhost";
-
-        if [[ `git remote -v` == *"upstream"* ]]; then
-            git remote remove upstream;
-        fi;
-        git remote add upstream "$UPSTREAM_URL:$UPSTREAM_PROJECT";
-      fi
+    - bash ./.ci/setup_ssh.sh
 
 
 ###################################################
@@ -197,11 +125,7 @@ variables:
 
 .patch_version: &patch_version
   before_script:
-
-    - if [[ "x$CI_COMMIT_TAG" != "x" ]]; then
-        echo "Release detected - patching version - $CI_COMMIT_REF_NAME";
-        python -c "import fsl.version as v; v.patchVersion('fsl/version.py', '$CI_COMMIT_REF_NAME')";
-      fi
+    - bash ./.ci/patch_version.sh
 
 
 ############
@@ -220,72 +144,7 @@ variables:
     - docker
 
   script:
-
-    # Install $PY_VERSION, xvfb, and all
-    # of the wxpython dependencies.
-    - apt-get update -y || true
-    - apt-get install -y software-properties-common python-software-properties xvfb libgtk2.0-0 libnotify4 freeglut3 libsdl1.2debian
-    - add-apt-repository -y ppa:deadsnakes/ppa
-    - apt-get update -y || true
-    - apt-get install -y $PY_VERSION "$PY_VERSION"-dev $PY_PACKAGES
-    - $PY_VENV test.venv
-    - source test.venv/bin/activate
-    - pip install --upgrade pip setuptools
-
-    # If running on a fork repository, we merge in the
-    # upstream/master branch. This is done so that merge
-    # requests from fork to the parent repository will
-    # have unit tests run on the merged code, something
-    # which gitlab CE does not currently do for us.
-    - if [[ "$CI_PROJECT_PATH" != "$UPSTREAM_PROJECT" ]]; then
-        git fetch upstream;
-        git merge --no-commit --no-ff upstream/master;
-      fi;
-
-    - $INSTALL_WX
-
-    # All other deps can be installed as normal.
-    # We install test dependenciesd through pip,
-    # because if we let setuptools do it, it
-    # will build/install everything from source,
-    # rather than using wheels.
-    - pip install -r requirements.txt
-    - pip install sphinx sphinx-rtd-theme
-    - pip install pytest pytest-cov pytest-html pytest-runner mock coverage
-
-    # style stage
-    - if [ "$TEST_STYLE"x != "x" ]; then pip install pylint flake8; fi;
-    - if [ "$TEST_STYLE"x != "x" ]; then flake8                           fsl || true; fi;
-    - if [ "$TEST_STYLE"x != "x" ]; then pylint --output-format=colorized fsl || true; fi;
-    - if [ "$TEST_STYLE"x != "x" ]; then exit 0; fi
-
-    # We need the FSL atlases for the atlas
-    # tests, and need $FSLDIR to be defined
-    - export FSLDIR=/fsl/
-    - mkdir -p $FSLDIR/data/
-    - rsync -rv "fsldownload:data/atlases/" "$FSLDIR/data/atlases/"
-
-    # Finally, run the damned tests.
-
-    # We run some tests under xvfb-run
-    # because they invoke wx. Sleep in
-    # between, otherwise xvfb gets upset.
-    - xvfb-run python setup.py test --addopts="$TEST_OPTS tests/test_idle.py"
-    - sleep 5
-    - xvfb-run python setup.py test --addopts="$TEST_OPTS tests/test_platform.py"
-
-    # We run the immv/imcpy tests as the nobody
-    # user because some tests expect permission
-    # denied errors when looking at files, and
-    # root never gets denied. Make everything in
-    # this directory writable by anybody (which,
-    # unintuitively, includes nobody)
-    - chmod -R a+w `pwd`
-    - su -s /bin/bash -c 'source test.venv/bin/activate && python setup.py test --addopts="$TEST_OPTS tests/test_immv_imcp.py"' nobody
-
-    # All other tests can be run as normal
-    - python setup.py test --addopts="$TEST_OPTS --ignore=tests/test_idle.py --ignore=tests/test_platform.py --ignore=tests/test_immv_imcp.py"
-    - python -m coverage report
+    - bash ./.ci/test_template.sh
 
 
 test:2.7:
@@ -366,8 +225,8 @@ build-doc:
   image: python:3.5
 
   script:
-    - python setup.py doc
-    - mv doc/html doc/"$CI_COMMIT_REF_NAME"
+    - bash ./.ci/build_doc.sh
+
   artifacts:
     expire_in: 1 day
     paths:
@@ -379,7 +238,7 @@ build-doc:
 #############
 
 
-build-dist:
+build-pypi-dist:
   <<: *only_releases
   <<: *patch_version
 
@@ -390,9 +249,27 @@ build-dist:
     - docker
 
   script:
-   - pip install wheel
-   - python setup.py sdist
-   - python setup.py bdist_wheel
+   - bash ./.ci/build_pypi_dist.sh
+
+  artifacts:
+    expire_in: 1 day
+    paths:
+      - dist/*
+
+
+build-conda-dist:
+  <<: *only_releases
+  <<: *patch_version
+
+  stage: build
+  image: continuumio/minconda
+
+  tags:
+    - docker
+
+  script:
+
+   - bash ./.ci/build_conda_dist.sh
 
   artifacts:
     expire_in: 1 day
@@ -419,7 +296,7 @@ deploy-doc:
     - build-doc
 
   script:
-    - rsync -rv doc/"$CI_COMMIT_REF_NAME" "docdeploy:"
+    - bash ./.ci/deploy_doc.sh
 
 
 deploy-pypi:
@@ -433,8 +310,7 @@ deploy-pypi:
     - docker
 
   dependencies:
-    - build-dist
+    - build-pypi-dist
 
   script:
-    - pip install setuptools wheel twine
-    - twine upload dist/*
+    - bash ./.ci/deploy_pypi.sh