Make Rosie Work under packaging (branched from #2360)

.bandit

@@ -1 +1 @@
-skips: ['B101']
+skips: ['B101', 'B322']

.eslintignore

@@ -1,6 +1,6 @@
 doc/*
-lib/html/static/js/bootstrap*
-lib/html/static/js/dataTables.bootstrap*
-lib/html/static/js/jquery*
-lib/html/static/js/livestamp.min.js
-lib/html/static/js/moment.min.js
+metomi/rosie/lib/html/static/js/bootstrap*
+metomi/rosie/lib/html/static/js/dataTables.bootstrap*
+metomi/rosie/lib/html/static/js/jquery*
+metomi/rosie/lib/html/static/js/livestamp.min.js
+metomi/rosie/lib/html/static/js/moment.min.js

.gitignore

@@ -5,6 +5,8 @@ etc/opt
 lib/bash/rose_init_site
 doc
 venv
+metomi_rose.egg-info
+dist
 
 # coverage
 .coverage

.travis.yml

@@ -20,20 +20,22 @@ jobs:
   include:
     - name: "Unit Tests"
       install:
-        - now install coverage cylc linters pytest rose
+        - now install coverage linters pytest cylc rose
       script:
         - now test style
         - now test units
 
     - name: "Test Battery"
       before_install:
         - export PATH="$PWD/.travis:$PATH"
-        - now install coverage cylc fcm rose rosie tut_suite
+        - now install coverage fcm tut_suite
+      install:
+        - now install isodatetime cylc rose
       script:
         - now test battery
+
     - name: "Documentation"
       install:
-        - now install coverage rose sphinx tut_suite
+        - now install coverage isodatetime rose sphinx tut_suite
       script:
         - now test docs
-        - now build docs

.travis/cover.py

@@ -24,7 +24,7 @@
 
 
 def main():
-    command = ['rose', 'test-battery', '-j', '5']
+    command = ['etc/bin/rose-test-battery', '-j', '5']
     if call(command + ['--state=save']):
         # Non-zero return code
         sys.stderr.write('\n\nRerunning Failed Tests...\n\n')

.travis/now

@@ -49,7 +49,7 @@ WANDISCO=false
 
 
 _build_docs () {
-    rose make-docs --strict clean html slides latexpdf
+    etc/bin/rose-make-docs --strict clean html slides latexpdf
 }
 
 _gh_extract () {  # extract project from GitHub to $HOME
@@ -79,12 +79,24 @@ _install_coverage () {
     PY_PATH+=("${TRAVIS_BUILD_DIR}/.travis")
 }
 
+_install_rose () {
+    pip install -e .
+    PY_PATH+=("${TRAVIS_BUILD_DIR}/metomi")
+    RC_PATH+=("${TRAVIS_BUILD_DIR}/bin")
+}
+
 _install_cylc () {
     APT+=(at heirloom-mailx)
     GIT+=('cylc|cylc-flow|master')
     RC_PATH+=("${HOME}/cylc-master/bin")
 }
 
+_install_isodatetime () {
+    wget 'https://github.com/metomi/isodatetime/archive/master.tar.gz' \
+        -O - | tar -xz -C "${HOME}"
+    pip install -e "${HOME}/isodatetime-master"
+}
+
 _install_fcm () {
     APT+=(subversion build-essential gfortran libxml-parser-perl \
           libconfig-inifiles-perl libdbi-perl libdbd-sqlite3-perl)
@@ -98,12 +110,6 @@ _install_pytest () {
     PIP+=(pytest)
 }
 
-_install_rose () {
-    PIP+=(aiofiles)
-    PY_PATH+=("${TRAVIS_BUILD_DIR}/lib/python/")
-    RC_PATH+=("${TRAVIS_BUILD_DIR}/bin")
-}
-
 _install_rosie () {
     PIP+=(requests tornado sqlalchemy)
     RI_PATH+=("$(_path_for python)" "$(_path_for rose)")
@@ -140,7 +146,7 @@ _path_for () {
 }
 
 _test_units () {
-    pytest --cov-append lib/python/rose/tests/*
+    pytest --cov-append metomi/rose/tests/*
 }
 
 _test_style () {
@@ -152,11 +158,10 @@ _test_style () {
 _test_battery () {
     cp "${TRAVIS_BUILD_DIR}/.travis/sitecustomize.py" ./lib/python
     coverage run .travis/cover.py
-    rm ./lib/python/sitecustomize.py
 }
 
 _test_docs () {
-    rose make-docs --strict clean linkcheck doctest
+    etc/bin/rose-make-docs --strict clean linkcheck doctest
 }
 
 _wandisco_configure () {  # extract Wandisco stuff

.travis/shellchecker

@@ -79,7 +79,7 @@ default () {
     main . \
         --exclude etc/rose-bash-completion \
         --exclude t \
-        -- -e SC1090
+        -- -e SC1090 -e SC2119
 
     # run a lenient check on all test scripts
     main t -- -S error -e SC1090

README.md

@@ -19,7 +19,7 @@ release for production use.
 
 [Installation](http://metomi.github.io/rose/doc/html/installation.html) |
 [User Guide](http://metomi.github.io/rose/) |
-[How to Contribute](CONTRIBUTING.md)
+[How to Contribute](https://github.com/metomi/rose/blob/master/CONTRIBUTING.md)
 
 ## Copyright and Terms of Use
 
@@ -46,4 +46,4 @@ See <http://metomi.github.io/rose/doc/html/terms.html>.
 
 ## Acknowledgement for non-Rose Work
 
-See [Acknowledgement for Non-Rose Work](ACKNOWLEDGEMENT.md).
+See [Acknowledgement for Non-Rose Work](https://github.com/metomi/rose/blob/master/ACKNOWLEDGEMENT.md).

bin/rose

@@ -37,7 +37,9 @@
 if ${ROSE_DEBUG:-false}; then
     set -x
 fi
-. "$(dirname "$0")/../lib/bash/rose_init"
+# shellcheck source=lib/bash/rose_init
+# shellcheck source=lib/bash/rose_usage
+. rose_init
 rose_init
 
 # Print actual command of a command alias
@@ -100,10 +102,11 @@ path_lead() {
 
 # Print Rose version
 function print_version() {
-    echo "Rose $ROSE_VERSION ($ROSE_HOME)"
+    echo "Rose $ROSE_VERSION ($ROSE_HOME_BIN)"
 }
 
 #-------------------------------------------------------------------------------
+# if "rose x" input then set UTIL=x
 UTIL="help"
 if (($# > 0)); then
     UTIL=$1
@@ -147,10 +150,8 @@ version|--version|-V)
     exit
     :;;
 doc)
-    PATH=$(path_lead "${PATH:-}" "$ROSE_HOME_BIN")
-    PYTHONPATH=$(path_lead "${PYTHONPATH:-}" "$ROSE_HOME/lib/python")
     ROSE_UTIL=$UTIL
-    export PATH PYTHONPATH ROSE_UTIL
+    export ROSE_UTIL
     ns_len=$(( ${#ROSE_NS}+2 ))
     for U in $(cd "$ROSE_HOME_BIN" && ls "$ROSE_NS-"*); do
         NAME="$(sed "s/^$ROSE_NS-\\(.*\\)\$/\1/" <<<"$U")"
@@ -185,8 +186,6 @@ if (($# > 0)) && [[ $1 == '--help' || $1 == '-h' ]]; then
     help_util "$UTIL"
     exit
 fi
-PATH=$(path_lead "${PATH:-}" "$ROSE_HOME_BIN")
-PYTHONPATH=$(path_lead "${PYTHONPATH:-}" "$ROSE_HOME/lib/python")
 ROSE_UTIL=$UTIL
-export PATH PYTHONPATH ROSE_UTIL
+export ROSE_UTIL
 exec "$COMMAND" "$@"

bin/rose-app-run

@@ -86,4 +86,4 @@
 #     optional ROSE_FILE_INSTALL_ROOT
 #         If specified, change to the specified directory to install files.
 #-------------------------------------------------------------------------------
-exec python3 -m rose.app_run "$@"
+exec python3 -m metomi.rose.app_run "$@"

bin/rose-app-upgrade

@@ -48,4 +48,4 @@
 #     optional ROSE_META_PATH
 #         Prepend `$ROSE_META_PATH` to the metadata search path.
 #-------------------------------------------------------------------------------
-exec python3 -m rose.upgrade "$@"
+exec python3 -m metomi.rose.upgrade "$@"

bin/rose-config

@@ -99,4 +99,4 @@
 #     optional ROSE_META_PATH
 #         Prepend `$ROSE_META_PATH` to the metadata search path.
 #-------------------------------------------------------------------------------
-exec python3 -m rose.config_cli "$@"
+exec python3 -m metomi.rose.config_cli "$@"

bin/rose-config-diff

@@ -114,4 +114,4 @@
 #           rose config-diff --ignore=namelist:bar --ignore=namelist:baz ...
 #
 #-------------------------------------------------------------------------------
-exec python3 -m rose.config_diff "$@"
+exec python3 -m metomi.rose.config_diff "$@"

bin/rose-config-dump

@@ -47,4 +47,4 @@
 #     --quiet, -q
 #         Decrement verbosity. Do not report modified files.
 #-------------------------------------------------------------------------------
-exec python3 -m rose.config_dump "$@"
+exec python3 -m metomi.rose.config_dump "$@"

bin/rose-config-edit

@@ -70,4 +70,4 @@
 #     optional ROSE_META_PATH
 #         Prepend `$ROSE_META_PATH` to the metadata search path.
 #-------------------------------------------------------------------------------
-exec python3 -m rose.config_editor.main "$@"
+exec python3 -m metomi.rose.config_editor.main "$@"

bin/rose-date

@@ -177,7 +177,7 @@ PRINT FORMAT
 import sys
 import os
 
-from isodatetime.main import main as iso_main
+from metomi.isodatetime.main import main as iso_main
 
 
 def main():

bin/rose-env-cat

@@ -48,4 +48,4 @@
 #         variable with the value of `STRING`, (which can be an empty string),
 #         instead of failing.
 #-------------------------------------------------------------------------------
-exec python3 -m rose.env_cat "$@"
+exec python3 -m metomi.rose.env_cat "$@"

bin/rose-host-select

@@ -91,4 +91,4 @@
 #        Set the timeout in seconds of SSH commands to hosts.
 #        (default=10.0)
 #-------------------------------------------------------------------------------
-exec python3 -m rose.host_select "$@"
+exec python3 -m metomi.rose.host_select "$@"

bin/rose-macro

@@ -76,4 +76,4 @@
 #     optional ROSE_META_PATH
 #         Prepend `$ROSE_META_PATH` to the metadata search path.
 #-------------------------------------------------------------------------------
-exec python3 -m rose.macro "$@"
+exec python3 -m metomi.rose.macro "$@"

bin/rose-metadata-check

@@ -40,4 +40,4 @@
 #        metadata e.g.`env=FOO` or `namelist:bar`. If specified, only
 #        this section will be checked.
 #-------------------------------------------------------------------------------
-exec python3 -m rose.metadata_check "$@"
+exec python3 -m metomi.rose.metadata_check "$@"

bin/rose-metadata-gen

@@ -46,4 +46,4 @@
 #        every setting e.g. `compulsory=true`. If `=VALUE` is missing,
 #        the property will be set to a null string in each setting.
 #-------------------------------------------------------------------------------
-exec python3 -m rose.metadata_gen "$@"
+exec python3 -m metomi.rose.metadata_gen "$@"

bin/rose-metadata-graph

@@ -50,4 +50,4 @@
 #     optional ROSE_META_PATH
 #         Prepend `$ROSE_META_PATH` to the metadata search path.
 #-------------------------------------------------------------------------------
-exec python3 -m rose.metadata_graph "$@"
+exec python3 -m metomi.rose.metadata_graph "$@"

bin/rose-mpi-launch

@@ -111,7 +111,8 @@
 # DIAGNOSTICS
 #     Return 0 on success, 1 or exit code of the launcher program on failure.
 #-------------------------------------------------------------------------------
-. "$(dirname "$0")/../lib/bash/rose_init"
+# shellcheck source=lib/bash/rose_init
+. rose_init
 rose_init rose_log
 
 # ------------------------------------------------------------------------------

bin/rose-namelist-dump

@@ -45,4 +45,4 @@
 #     -u, --upper
 #         Shorthand for `--case=upper`.
 #-------------------------------------------------------------------------------
-exec python3 -m rose.namelist_dump "$@"
+exec python3 -m metomi.rose.namelist_dump "$@"

bin/rose-stem

@@ -82,4 +82,4 @@
 #         is intended to specify the revision of `fcm-make` config files.
 #
 #-------------------------------------------------------------------------------
-exec python3 -m rose.stem "$@"
+exec python3 -m metomi.rose.stem "$@"

bin/rose-suite-clean

@@ -50,4 +50,4 @@
 #     Return the difference between the number of arguments and number of
 #     successfully cleaned suites, i.e. 0 if all successful.
 #-------------------------------------------------------------------------------
-exec python3 -m rose.suite_clean "$@"
+exec python3 -m metomi.rose.suite_clean "$@"

bin/rose-suite-cmp-vc

@@ -50,4 +50,4 @@
 #     --verbose, -v
 #         Increment verbosity.
 #-------------------------------------------------------------------------------
-exec python3 -m rose.cmp_source_vc "$@"
+exec python3 -m metomi.rose.cmp_source_vc "$@"

bin/rose-suite-hook

@@ -51,4 +51,4 @@
 #     --verbose, -v
 #         Increment verbosity.
 #-------------------------------------------------------------------------------
-exec python3 -m rose.suite_hook "$@"
+exec python3 -m metomi.rose.suite_hook "$@"

bin/rose-suite-log

@@ -64,4 +64,4 @@
 #     --view
 #         Launch web browser to view suite log.
 #-------------------------------------------------------------------------------
-exec python3 -m rose.suite_log "$@"
+exec python3 -m metomi.rose.suite_log "$@"

bin/rose-suite-restart

@@ -55,4 +55,4 @@
 #     --verbose, -v
 #         Increment verbosity.
 #-------------------------------------------------------------------------------
-exec python3 -m rose.suite_restart "$@"
+exec python3 -m metomi.rose.suite_restart "$@"

bin/rose-suite-run

@@ -129,4 +129,4 @@
 #     * `cylc help register`
 #     * `cylc help run`
 #-------------------------------------------------------------------------------
-exec python3 -m rose.suite_run "$@"
+exec python3 -m metomi.rose.suite_run "$@"

bin/rose-suite-shutdown

@@ -54,4 +54,4 @@
 #         See the cylc documentation, cylc shutdown for options and details on 
 #         `EXTRA-ARGS`.
 #-------------------------------------------------------------------------------
-exec python3 -m rose.suite_control shutdown "$@"
+exec python3 -m metomi.rose.suite_control shutdown "$@"

bin/rose-task-env

@@ -140,4 +140,4 @@
 #     `env-script = eval $(rose task-env)`.
 #
 #-------------------------------------------------------------------------------
-exec python3 -m rose.task_env "$@"
+exec python3 -m metomi.rose.task_env "$@"

bin/rose-task-run

@@ -54,4 +54,4 @@
 #     * `rose app-run`
 #     * `rose task-env`
 #-------------------------------------------------------------------------------
-exec python3 -m rose.task_run "$@"
+exec python3 -m metomi.rose.task_run "$@"

bin/rose-tutorial

@@ -30,7 +30,8 @@
 #     Make a copy of one of the tutorial SUITE in the cylc-run directory.
 #
 #-------------------------------------------------------------------------------
-. "$(dirname "$0")/../lib/bash/rose_init"
+# shellcheck source=lib/bash/rose_init
+. rose_init
 mkdir -p "$HOME/cylc-run"
 
 usage () {

bin/rosie-checkout

@@ -38,4 +38,4 @@
 #     --verbose, -v
 #         Increment verbosity.
 #-------------------------------------------------------------------------------
-exec python3 -m rosie.vc checkout "$@"
+exec python3 -m metomi.rosie.vc checkout "$@"

bin/rosie-create

@@ -70,4 +70,4 @@
 #     --verbose, -v
 #         Increment verbosity.
 #-------------------------------------------------------------------------------
-exec python3 -m rosie.vc create "$@"
+exec python3 -m metomi.rosie.vc create "$@"

bin/rosie-delete

@@ -49,4 +49,4 @@
 #     --verbose, -v
 #         Increment verbosity.
 #-------------------------------------------------------------------------------
-exec python3 -m rosie.vc delete "$@"
+exec python3 -m metomi.rosie.vc delete "$@"

bin/rosie-disco

@@ -38,4 +38,4 @@
 #     --service-root, -R
 #         (For start only.) Include web service name under root of URL.
 #-------------------------------------------------------------------------------
-exec python3 -m rosie.ws "$@"
+exec python3 -m metomi.rosie.ws "$@"

bin/rosie-go

@@ -67,5 +67,5 @@
 #     * `rosie lookup`
 #     * `rosie ls`
 #-------------------------------------------------------------------------------
-exec python3 -m rosie.browser.main "$@"
+exec python3 -m metomi.rosie.browser.main "$@"