Merge pull request #22 from guerler/remove_mako_preferences_revision

Remove mako preferences revision

.ci/flake8_blacklist.txt

@@ -1,8 +1,8 @@
 .venv/
 .tox/
-eggs/
-client/
+client/node_modules/
 database/
 doc/patch.py
 doc/source/conf.py
+eggs/
 lib/galaxy/util/jstree.py

.ci/flake8_docstrings_include_list.txt

@@ -0,0 +1,2 @@
+lib/galaxy/jobs/metrics
+lib/galaxy/exceptions

.ci/flake8_lint_include_list.txt

@@ -1,8 +1,10 @@
+client/galaxy/style/source_material/circle.py
 contrib/
 cron/add_manual_builds.py
 cron/cleanup_datasets.py
 cron/parse_builds_3_sites.py
 cron/parse_builds.py
+doc/parse_gx_xsd.py
 lib/galaxy/actions/
 lib/galaxy/auth/__init__.py
 lib/galaxy/auth/providers/__init__.py
@@ -101,6 +103,7 @@ lib/galaxy/managers/libraries.py
 lib/galaxy/managers/secured.py
 lib/galaxy/managers/taggable.py
 lib/galaxy/model/__init__.py
+lib/galaxy/model/mapping.py
 lib/galaxy/model/migrate/__init__.py
 lib/galaxy/model/migrate/versions/0001_initial_tables.py
 lib/galaxy/model/migrate/versions/0002_metadata_file_table.py
@@ -439,34 +442,47 @@ scripts/tool_shed/migrate_tools_to_repositories.py
 scripts/tool_shed/show_tool_dependency_installation_dir_contents.py
 scripts/tools/re_escape_output.py
 test/api/__init__.py
+test/api/test_dataset_collections.py
 test/api/test_datasets.py
 test/api/test_datatypes.py
 test/api/test_framework.py
 test/api/test_histories.py
 test/api/test_history_contents_provenance.py
 test/api/test_jobs.py
 test/api/test_libraries.py
+test/api/test_page_revisions.py
 test/api/test_search.py
+test/api/test_tool_data.py
+test/api/test_tools.py
 test/api/test_tours.py
+test/api/test_workflow_extraction.py
 test/api/test_workflows_from_yaml.py
-test/api/workflows_format_2/interface.py
-test/api/workflows_format_2/main.py
+test/api/workflows_format_2/
 test/base/api_asserts.py
+test/base/api.py
 test/base/api_util.py
 test/base/__init__.py
 test/base/instrument.py
+test/base/integration_util.py
+test/base/interactor.py
 test/base/nose_util.py
+test/base/test_logging.py
 test/base/tool_shed_util.py
+test/base/twilltestcase.py
 test/casperjs/
 test/functional/database_contexts.py
 test/functional/__init__.py
+test/functional/test_data_managers.py
+test/functional/test_toolbox.py
+test/functional/tool-data/
 test/functional/tools/
-test/integration/__init__.py
-test/integration/test_pulsar_embedded.py
+test/functional/workflow.py
+test/integration/
 test/manual/__init__.py
 test/shed_functional/base/common.py
 test/shed_functional/base/__init__.py
 test/shed_functional/functional/
+test/shed_functional/functional_tests.py
 test/shed_functional/__init__.py
 test/unit/dataset_collections/__init__.py
 test/unit/datatypes/dataproviders/__init__.py
@@ -515,54 +531,4 @@ test/unit/workflows/test_render.py
 test/unit/workflows/test_workflow_progress.py
 test/unit/test_objectstore.py
 tool_list.py
-tools/data_source/fetch.py
-tools/data_source/genbank.py
-tools/data_source/hbvar_filter.py
-tools/data_source/import.py
-tools/data_source/microbial_import_code.py
-tools/data_source/microbial_import.py
-tools/data_source/upload.py
-tools/evolution/
-tools/extract/liftOver_wrapper.py
-tools/filters/axt_to_concat_fasta.py
-tools/filters/axt_to_fasta.py
-tools/filters/axt_to_lav_code.py
-tools/filters/axt_to_lav.py
-tools/filters/bed_to_gff_converter.py
-tools/filters/catWrapper.py
-tools/filters/convert_characters.py
-tools/filters/gff/
-tools/filters/gff_to_bed_converter.py
-tools/filters/gtf_to_bedgraph_converter.py
-tools/filters/join.py
-tools/filters/joinWrapper.py
-tools/filters/lav_to_bed_code.py
-tools/filters/lav_to_bed.py
-tools/filters/mergeCols.py
-tools/filters/randomlines.py
-tools/filters/random_lines_two_pass.py
-tools/filters/secure_hash_message_digest.py
-tools/filters/sff_extract.py
-tools/filters/sorter.py
-tools/filters/trimmer.py
-tools/filters/ucsc_gene_bed_to_exon_bed.py
-tools/filters/ucsc_gene_bed_to_intron_bed.py
-tools/filters/ucsc_gene_table_to_intervals.py
-tools/filters/uniq.py
-tools/filters/wiggle_to_simple.py
-tools/genomespace/
-tools/maf/
-tools/meme/
-tools/metag_tools/
-tools/next_gen_conversion/fastq_conversions.py
-tools/next_gen_conversion/fastq_gen_conv.py
-tools/next_gen_conversion/solid_to_fastq.py
-tools/ngs_simulation/
-tools/phenotype_association/
-tools/plotting/
-tools/solid_tools/
-tools/sr_assembly/
-tools/sr_mapping/
-tools/stats/grouping.py
-tools/stats/gsummary.py
-tools/visualization/
+tools/

.ci/flake8_wrapper.sh

@@ -5,4 +5,4 @@ set -e
 flake8 --exclude `paste -sd, .ci/flake8_blacklist.txt` .
 
 # Apply stricter rules for the directories shared with Pulsar
-flake8 --ignore= --max-line-length=150 lib/galaxy/jobs/runners/util/
+flake8 --ignore=D --max-line-length=150 lib/galaxy/jobs/runners/util/

.ci/flake8_wrapper_docstrings.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+
+set -e
+
+# D100 - Missing docstring in public module.
+# D2XX - Whitespace issues.
+# D3XX - Quoting issues.
+# D401 - First line should be in imperative mood 
+# D403 - First word of the first line should be properly capitalized
+args="--ignore=D --select=D100,D201,D202,D206,D207,D208,D209,D211,D3,D401,D403"
+
+# If the first argument is --include, lint the modules expected to pass. If
+# the first argument is --exclude, lint all modules the full Galaxy linter lints
+# (this will fail).
+
+if [ "$1" = "--include" ];
+then
+    flake8 $args `paste .ci/flake8_docstrings_include_list.txt`
+else
+    flake8 $args --exclude `paste -sd, .ci/flake8_blacklist.txt` .
+fi

.ci/py3_sources.txt

@@ -1,5 +1,7 @@
+client/galaxy/style/source_material/circle.py
 contrib/
 cron/
+doc/parse_gx_xsd.py
 lib/galaxy/actions/
 lib/galaxy/auth/
 lib/galaxy/config.py
@@ -26,6 +28,7 @@ lib/galaxy/forms/
 lib/galaxy/jobs/
 lib/galaxy/managers/
 lib/galaxy/model/__init__.py
+lib/galaxy/model/mapping.py
 lib/galaxy/model/migrate/
 lib/galaxy/objectstore/
 lib/galaxy/openid/
@@ -71,8 +74,4 @@ scripts/db_shell.py
 scripts/drmaa_external_runner.py
 test/
 tool_list.py
-tools/data_source/
-tools/evolution/
-tools/sr_mapping/
-tools/stats/aggregate_scores_in_intervals.py
-tools/visualization/
+tools/

.travis.yml

@@ -11,6 +11,7 @@ env:
   - TOX_ENV=py27-lint-imports
   - TOX_ENV=py27-lint-imports-include-list
   - TOX_ENV=validate-test-tools
+  - TOX_ENV=py27-lint-docstring-include-list
 
 matrix:
   include:
@@ -23,9 +24,6 @@ matrix:
   allow_failures:
   - env: TOX_ENV=py27-lint-imports
 
-before_install:
-  - if [ `uname` == "Darwin"  ]; then bash -c "brew update && brew install python"; fi
-
 install:
   - pip install tox
   - if [ "$TOX_ENV" == "validate-test-tools" ]; then sudo apt-get install libxml2-utils; fi

client/galaxy/scripts/mvc/form/form-section.js

@@ -104,7 +104,7 @@ function( Utils, Ui, Portlet, Repeat, InputElement, Parameters ) {
             // add parsed/minimum number of repeat blocks
             //
             var n_cache = _.size( input_def.cache );
-            for ( var i = 0; i < Math.max( Math.max( n_cache, input_def.min ), input_def.default || 0 ); i++ ) {
+            for ( var i = 0; i < Math.max( Math.max( n_cache, input_def.min || 0 ), input_def.default || 0 ); i++ ) {
                 create( i < n_cache ? input_def.cache[ i ] : input_def.inputs );
             }
 

client/galaxy/scripts/mvc/tool/tool-form-base.js

@@ -16,12 +16,14 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
                     self._buildModel(process, options, true);
                 });
             }
-            // Listen to history panel
+            // listen to history panel
             if ( options.listen_to_history && parent.Galaxy && parent.Galaxy.currHistoryPanel ) {
                 this.listenTo( parent.Galaxy.currHistoryPanel.collection, 'change', function() {
                     this.refresh();
                 });
             }
+            // destroy dom elements
+            this.$el.on( 'remove', function() { self.remove() } );
         },
 
         /** Listen to history panel changes and update the tool form */
@@ -101,9 +103,9 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
                     Galaxy.emit.debug('tool-form-base::initialize()', 'Initial tool model ready.', new_model);
                     process.resolve();
                 },
-                error   : function(response, xhr) {
+                error   : function(response, status) {
                     var error_message = ( response && response.err_msg ) || 'Uncaught error.';
-                    if ( xhr.status == 401 ) {
+                    if ( status == 401 ) {
                         window.location = Galaxy.root + 'user/login?' + $.param({ redirect : Galaxy.root + '?tool_id=' + self.options.id });
                     } else if ( self.$el.is(':empty') ) {
                         self.$el.prepend((new Ui.Message({