Create release 0.75.30

Author: mvdbeek

HISTORY.rst

@@ -6,8 +6,19 @@ History
 .. to_doc
 
 ---------------------
-0.75.30.dev0
+0.75.30 (2025-05-07)
 ---------------------
+* fix lint_shed_version if there are no installable revisions (thanks to
+  `@bernt-matthias`_). `Pull Request 1509`_
+* Fix bumping of dev versions (thanks to `@mvdbeek`_). `Pull Request 1514`_
+* Don't escape non-ascii unicode characters in json.dumps (thanks to
+  `@mvdbeek`_). `Pull Request 1523`_
+* Fix version linter for new repos (thanks to `@bernt-matthias`_). `Pull
+  Request 1519`_
+* Add switch to prevent early termination of workflow runs (thanks to
+  `@kostrykin`_). `Pull Request 1518`_
+* Add missing collection operation tools (thanks to `@mvdbeek`_). `Pull
+  Request 1524`_
 
 ---------------------
 0.75.29 (2025-03-27)
@@ -2195,6 +2206,12 @@ History
   tools - and more experimental features involving Docker and Homebrew. 7d07782_
 
 .. github_links
+.. _Pull Request 1509: https://github.com/galaxyproject/planemo/pull/1509
+.. _Pull Request 1514: https://github.com/galaxyproject/planemo/pull/1514
+.. _Pull Request 1523: https://github.com/galaxyproject/planemo/pull/1523
+.. _Pull Request 1519: https://github.com/galaxyproject/planemo/pull/1519
+.. _Pull Request 1518: https://github.com/galaxyproject/planemo/pull/1518
+.. _Pull Request 1524: https://github.com/galaxyproject/planemo/pull/1524
 .. _Pull Request 1507: https://github.com/galaxyproject/planemo/pull/1507
 .. _Pull Request 1505: https://github.com/galaxyproject/planemo/pull/1505
 .. _Pull Request 1504: https://github.com/galaxyproject/planemo/pull/1504
@@ -3171,3 +3188,4 @@ History
 .. _@jdavcs: https://github.com/jdavcs
 .. _@Smeds: https://github.com/Smeds
 .. _@jmchilton: https://github.com/jmchilton
+.. _@kostrykin: https://github.com/kostrykin

docs/commands/clone.rst

@@ -18,14 +18,13 @@ For instance, the following will clone, fork, and branch the tools-iuc
 repository to allow a subsequent pull request to fix a problem with bwa.
 
 
-::
-
-    $ planemo clone --branch bwa-fix tools-iuc
-    $ cd tools-iuc
-    $ # Make changes.
-    $ git add -p # Add desired changes.
-    $ git commit -m "Fix bwa problem."
-    $ planemo pull_request -m "Fix bwa problem."
+
+$ planemo clone --branch bwa-fix tools-iuc
+$ cd tools-iuc
+$ # Make changes.
+$ git add -p # Add desired changes.
+$ git commit -m "Fix bwa problem."
+$ planemo pull_request -m "Fix bwa problem."
 
 These changes do require that a github access token is
 specified in ~/.planemo.yml. An access token can be generated by going

docs/commands/conda_env.rst

@@ -17,14 +17,13 @@ Activate a conda environment for tool.
 Source the output of this command to activate a conda environment for this
 tool.
 
-::
-
-    $ . <(planemo conda_env seqtk_seq.xml)
-    Deactivate environment with conda_env_deactivate
-    (seqtk_seq_v6) $ which seqtk
-    /home/planemo/miniconda2/envs/jobdepsDkzcjjfecc6d406196737781ff4456ec60975c137e04884e4f4b05dc68192f7cec4656/bin/seqtk
-    (seqtk_seq_v6) $ conda_env_deactivate
-    $
+
+$ . <(planemo conda_env seqtk_seq.xml)
+Deactivate environment with conda_env_deactivate
+(seqtk_seq_v6) $ which seqtk
+/home/planemo/miniconda2/envs/jobdepsDkzcjjfecc6d406196737781ff4456ec60975c137e04884e4f4b05dc68192f7cec4656/bin/seqtk
+(seqtk_seq_v6) $ conda_env_deactivate
+$
 
 
 **Options**::

docs/commands/database_create.rst

@@ -33,14 +33,13 @@ distros this file is in /etc/postgresql/<postgres_version>/main/ directory).
 Adding the following lines to that file will allow planemo and Galaxy to
 access the databases without a password.
 
-::
-
-    # "local" is for Unix domain socket connections only
-    local   all   all                    trust
-    # IPv4 local connections:
-    host    all   all    127.0.0.1/32    trust
-    # IPv6 local connections:
-    host    all   all    ::1/128         trust
+
+# "local" is for Unix domain socket connections only
+local   all   all                    trust
+# IPv4 local connections:
+host    all   all    127.0.0.1/32    trust
+# IPv6 local connections:
+host    all   all    ::1/128         trust
 
 More information on the ``pg_hda.conf`` configuration file can be found at
 http://www.postgresql.org/docs/9.3/static/auth-pg-hba-conf.html.
@@ -50,9 +49,8 @@ http://www.postgresql.org/docs/9.4/static/libpq-pgpass.html. In Ubuntu and
 Debian distros - a postgres user likely already exists and its password can
 be set by setting up a file ``~/.pgpass`` file with the following contents.
 
-::
-
-    *:*:*:postgres:<postgres_password>
+
+*:*:*:postgres:<postgres_password>
 
 **Options**::
 

docs/commands/database_delete.rst

@@ -33,14 +33,13 @@ distros this file is in /etc/postgresql/<postgres_version>/main/ directory).
 Adding the following lines to that file will allow planemo and Galaxy to
 access the databases without a password.
 
-::
-
-    # "local" is for Unix domain socket connections only
-    local   all   all                    trust
-    # IPv4 local connections:
-    host    all   all    127.0.0.1/32    trust
-    # IPv6 local connections:
-    host    all   all    ::1/128         trust
+
+# "local" is for Unix domain socket connections only
+local   all   all                    trust
+# IPv4 local connections:
+host    all   all    127.0.0.1/32    trust
+# IPv6 local connections:
+host    all   all    ::1/128         trust
 
 More information on the ``pg_hda.conf`` configuration file can be found at
 http://www.postgresql.org/docs/9.3/static/auth-pg-hba-conf.html.
@@ -50,9 +49,8 @@ http://www.postgresql.org/docs/9.4/static/libpq-pgpass.html. In Ubuntu and
 Debian distros - a postgres user likely already exists and its password can
 be set by setting up a file ``~/.pgpass`` file with the following contents.
 
-::
-
-    *:*:*:postgres:<postgres_password>
+
+*:*:*:postgres:<postgres_password>
 
 **Options**::
 

docs/commands/database_list.rst

@@ -33,14 +33,13 @@ distros this file is in /etc/postgresql/<postgres_version>/main/ directory).
 Adding the following lines to that file will allow planemo and Galaxy to
 access the databases without a password.
 
-::
-
-    # "local" is for Unix domain socket connections only
-    local   all   all                    trust
-    # IPv4 local connections:
-    host    all   all    127.0.0.1/32    trust
-    # IPv6 local connections:
-    host    all   all    ::1/128         trust
+
+# "local" is for Unix domain socket connections only
+local   all   all                    trust
+# IPv4 local connections:
+host    all   all    127.0.0.1/32    trust
+# IPv6 local connections:
+host    all   all    ::1/128         trust
 
 More information on the ``pg_hda.conf`` configuration file can be found at
 http://www.postgresql.org/docs/9.3/static/auth-pg-hba-conf.html.
@@ -50,9 +49,8 @@ http://www.postgresql.org/docs/9.4/static/libpq-pgpass.html. In Ubuntu and
 Debian distros - a postgres user likely already exists and its password can
 be set by setting up a file ``~/.pgpass`` file with the following contents.
 
-::
-
-    *:*:*:postgres:<postgres_password>
+
+*:*:*:postgres:<postgres_password>
 
 **Options**::
 

docs/commands/docker_build.rst

@@ -24,10 +24,9 @@ This command will then build and tag the image so it is ready to be tested
 and published. The docker_shell command be used to test out the built
 image.
 
-::
-
-    % planemo docker_build bowtie2.xml # asssumes Dockerfile in same dir
-    % planemo docker_shell --from_tag bowtie2.xml
+
+% planemo docker_build bowtie2.xml # asssumes Dockerfile in same dir
+% planemo docker_shell --from_tag bowtie2.xml
 
 This can optionally also cache the images.
 

docs/commands/docker_shell.rst

@@ -18,11 +18,10 @@ Will launch a shell in the Docker container referenced by the specified
 tool. Prints a command to do this the way Galaxy would in job files it
 generates - so be sure to wrap this in $(...) to launch the subshell.
 
-::
-
-    $ $(planemo docker_shell bowtie2.xml)
-    ...
-    root@b8754062f875:/#
+
+$ $(planemo docker_shell bowtie2.xml)
+...
+root@b8754062f875:/#
 
 
 **Options**::

docs/commands/normalize.rst

@@ -22,17 +22,16 @@ the output as is - it frequently makes tool less readable not more.
 The top-level blocks will be reordered and whitespace fixed according to
 the tool development best practices outlined on the Galaxy wiki.
 
-::
-
-    % # Print normalized version of tool.
-    % planemo normalize tool.xml
-    <tool>
-    ...
-    % # Print a variant of tool with all macros expanded out, useful for
-    % # debugging complex macros.
-    % planemo normalize --expand_macros tool.xml
-    <tool>
-    ...
+
+% # Print normalized version of tool.
+% planemo normalize tool.xml
+<tool>
+...
+% # Print a variant of tool with all macros expanded out, useful for
+% # debugging complex macros.
+% planemo normalize --expand_macros tool.xml
+<tool>
+...
 
 **Options**::
 

docs/commands/pull_request.rst

@@ -17,14 +17,13 @@ Short-cut to quickly create a pull request for a relevant Github repo.
 For instance, the following will clone, fork, and branch the tools-iuc
 repository to allow a subsequent pull request to fix a problem with bwa.
 
-::
-
-    $ planemo clone --branch bwa-fix tools-iuc
-    $ cd tools-iuc
-    $ # Make changes.
-    $ git add -p # Add desired changes.
-    $ git commit -m "Fix bwa problem."
-    $ planemo pull_request -m "Fix bwa problem."
+
+$ planemo clone --branch bwa-fix tools-iuc
+$ cd tools-iuc
+$ # Make changes.
+$ git add -p # Add desired changes.
+$ git commit -m "Fix bwa problem."
+$ planemo pull_request -m "Fix bwa problem."
 
 These changes do require that a github access token is
 specified in ~/.planemo.yml. An access token can be generated by going