Merge branch 'release_22.05' into dev

galaxyproject · Dec 9, 2022 · ee7d51f · ee7d51f
2 parents 3b40e9a + 8ff59d4
commit ee7d51f
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Showing 27 changed files with 112 additions and 28 deletions.
diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst
@@ -4,11 +4,10 @@ History
 .. to_doc
 
 ---------------------
-20.9.1.dev0
+22.5.0.dev0
 ---------------------
 
 
-
 ---------------------
 20.9.0 (2020-10-15)
 ---------------------

diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg
@@ -54,7 +54,8 @@ install_requires =
     lxml
     Mako
     Markdown
-    packaging
+    MarkupSafe
+    packaging<22
     paramiko!=2.9.0,!=2.9.1
     pebble
     pulsar-galaxy-lib>=0.15.0.dev0

diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst
@@ -4,11 +4,10 @@ History
 .. to_doc
 
 ---------------------
-20.9.1.dev0
+22.5.0.dev0
 ---------------------
 
 
-
 ---------------------
 20.9.0 (2020-10-15)
 ---------------------

diff --git a/packages/build_packages.sh b/packages/build_packages.sh
@@ -0,0 +1,42 @@
+#!/bin/bash
+
+# Builds packages, sets new versions, but doesn't upload anything to pypi.
+# Set DEV_RELEASE=1 to build the dev of packages.
+
+set -ex
+
+# Change to packages directory.
+cd "$(dirname "$0")"
+
+# ensure ordered by dependency dag
+PACKAGE_DIRS=(
+    util
+    objectstore
+    job_metrics
+    config
+    files
+    tool_util
+    data
+    job_execution
+    auth
+    web_stack
+    web_framework
+    app
+    webapps
+    test_base
+    test_driver
+    test_api
+)
+for ((i=0; i<${#PACKAGE_DIRS[@]}; i++)); do
+    printf "\n========= RELEASING PACKAGE ${PACKAGE_DIRS[$i]} =========\n\n"
+    package_dir=${PACKAGE_DIRS[$i]}
+
+    cd "$package_dir"
+
+    make clean
+    make commit-version
+    make dist
+    make new-version
+
+    cd ..
+done
diff --git a/packages/config/HISTORY.rst b/packages/config/HISTORY.rst
@@ -3,6 +3,11 @@ History
 
 .. to_doc
 
+---------------------
+22.5.0.dev0
+---------------------
+
+
 ---------------------
 22.1.0.dev0
 ---------------------

diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst
@@ -4,7 +4,7 @@ History
 .. to_doc
 
 ---------------------
-20.9.1 (2021-03-02)
+22.5.0.dev0
 ---------------------
 
 

diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg
@@ -37,11 +37,11 @@ install_requires =
     alembic
     bdbag
     bx-python
-    contextvars; python_version >= "3.6" and python_version < "3.7"
     dnspython
     galaxy-sequence-utils
     h5py
     isa-rwval
+    MarkupSafe
     mrcfile
     numpy
     parsley
@@ -53,7 +53,7 @@ install_requires =
     rocrate
     social-auth-core[openidconnect]==4.0.3
     SQLAlchemy>=1.4.25,<2
-    tifffile<=2020.9.3  # Last version compatible with python 3.6
+    tifffile
     typing-extensions
     WebOb
 packages = find:

diff --git a/packages/files/HISTORY.rst b/packages/files/HISTORY.rst
@@ -4,7 +4,13 @@ History
 .. to_doc
 
 ---------------------
-22.1.0.dev0
+22.5.0.dev0
+---------------------
+
+
+
+---------------------
+22.1.0
 ---------------------
 
 * Initial standalone release of this package.
diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst
@@ -4,7 +4,7 @@ History
 .. to_doc
 
 ---------------------
-20.9.1.dev0
+22.5.0.dev0
 ---------------------
 
 

diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst
@@ -4,7 +4,7 @@ History
 .. to_doc
 
 ---------------------
-20.9.1.dev0
+22.5.0.dev0
 ---------------------
 
 

diff --git a/packages/meta/HISTORY.rst b/packages/meta/HISTORY.rst
@@ -4,7 +4,13 @@ History
 .. to_doc
 
 ---------------------
-19.9.0.dev0
+22.5.0.dev0
+---------------------
+
+
+
+---------------------
+19.9.0
 ---------------------
 
 * Initial import from dev branch of Galaxy during 19.09 development cycle.
diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst
@@ -4,7 +4,7 @@ History
 .. to_doc
 
 ---------------------
-20.9.2.dev0
+22.5.0.dev0
 ---------------------
 
 
@@ -13,7 +13,7 @@ History
 20.9.1 (2021-03-01)
 ---------------------
 
-
+* Second release from the 20.09 branch of Galaxy.
 
 ---------------------
 20.9.0 (2020-10-15)

diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst
@@ -4,7 +4,7 @@ History
 .. to_doc
 
 ---------------------
-20.9.1.dev0
+22.5.0.dev0
 ---------------------
 
 

diff --git a/packages/test_api/HISTORY.rst b/packages/test_api/HISTORY.rst
@@ -4,7 +4,7 @@ History
 .. to_doc
 
 ---------------------
-20.9.1.dev0
+22.5.0.dev0
 ---------------------
 
 
@@ -14,4 +14,3 @@ History
 ---------------------
 
 * Initial import from dev branch of Galaxy during 20.09 branch of Galaxy.
-
diff --git a/packages/test_base/HISTORY.rst b/packages/test_base/HISTORY.rst
@@ -4,7 +4,7 @@ History
 .. to_doc
 
 ---------------------
-20.9.1.dev0
+22.5.0.dev0
 ---------------------
 
 

diff --git a/packages/test_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst
@@ -4,7 +4,7 @@ History
 .. to_doc
 
 ---------------------
-20.9.1.dev0
+22.5.0.dev0
 ---------------------
 
 

diff --git a/packages/test_selenium/HISTORY.rst b/packages/test_selenium/HISTORY.rst
@@ -4,7 +4,7 @@ History
 .. to_doc
 
 ---------------------
-20.9.1.dev0
+22.5.0.dev0
 ---------------------
 
 

diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst
@@ -3,6 +3,13 @@ History
 
 .. to_doc
 
+-------------------
+22.5.0.dev0
+-------------------
+
+
+
+-------------------
 22.1.5 (2022-11-14)
 -------------------
 

diff --git a/packages/tool_util/setup.cfg b/packages/tool_util/setup.cfg
@@ -34,7 +34,7 @@ install_requires =
     galaxy-util>=22.1
     lxml
     MarkupSafe
-    packaging
+    packaging<22
     pydantic
     PyYAML
     requests

diff --git a/packages/util/HISTORY.rst b/packages/util/HISTORY.rst
@@ -3,6 +3,12 @@ History
 
 .. to_doc
 
+---------------------
+22.5.0.dev0
+---------------------
+
+
+
 ---------------------
 22.1.2 (2022-12-08)
 ---------------------

diff --git a/packages/util/setup.cfg b/packages/util/setup.cfg
@@ -35,9 +35,7 @@ install_requires =
     boltons
     docutils
     importlib_resources
-    MarkupSafe
     packaging<22  # packaging 22.0 dropped LegacyVersion
-    pycryptodome
     pyparsing
     PyYAML
     requests

diff --git a/packages/web_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst
@@ -4,7 +4,7 @@ History
 .. to_doc
 
 ---------------------
-20.9.1.dev0
+22.5.0.dev0
 ---------------------
 
 

diff --git a/packages/web_stack/HISTORY.rst b/packages/web_stack/HISTORY.rst
@@ -4,7 +4,7 @@ History
 .. to_doc
 
 ---------------------
-20.5.1.dev0
+22.5.0.dev0
 ---------------------
 
 

diff --git a/packages/webapps/HISTORY.rst b/packages/webapps/HISTORY.rst
@@ -4,7 +4,7 @@ History
 .. to_doc
 
 ---------------------
-20.5.1.dev0
+22.5.0.dev0
 ---------------------
 
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -70,6 +70,7 @@ Mercurial = "*"
 mrcfile = "*"
 nodeenv = "*"
 numpy = "*"
+packaging = "<22"  # packaging 22.0 dropped LegacyVersion
 paramiko = "!=2.9.0, !=2.9.1"  # https://github.com/paramiko/paramiko/issues/1961
 Parsley = "*"
 Paste = "*"

diff --git a/scripts/bootstrap_history.py b/scripts/bootstrap_history.py
@@ -206,6 +206,14 @@
 
           make release-create-rc
 
+    - [ ] Create dev packages:
+
+          cd packages && DEV_RELEASE=1 ./build_packages.sh
+
+
+    - [ ] Review created packages (HISTORY.rst correct, setup.cfg correct, correct version in filename)
+    - [ ] Upload galaxy-util & galaxy-tool-util dev packages to pypi
+    - [ ] Open PR against planemo with a pin to the dev packages
     - [ ] Open PRs from your fork of branch ``version-${version}`` to upstream ``release_${version}`` and of ``version-${next_version}.dev`` to ``dev``.
     - [ ] Update ``MILESTONE_NUMBER`` in the [maintenance bot](https://github.com/galaxyproject/galaxy/blob/dev/.github/workflows/maintenance_bot.yaml) to `${next_version}` so it properly tags new PRs.
 
@@ -263,6 +271,13 @@
 
           make release-create
 
+    - [ ] Create dev packages:
+
+          cd packages && ./build_packages.sh
+
+
+    - [ ] Review created packages (HISTORY.rst correct, setup.cfg correct, correct version in filename)
+    - [ ] Upload built packages to pypi
     - [ ] Add the branch `*/release_{version}` to Jenkins documentation build [configuration matrix](https://jenkins.galaxyproject.org/job/galaxy-sphinx-by-branch/configure).
     - [ ] Trigger the [branch documentation build](https://jenkins.galaxyproject.org/job/galaxy-sphinx-by-branch/)
     - [ ] Verify that everything is merged from ${version}->master, and then trigger the ['latest' documentation build](https://jenkins.galaxyproject.org/job/latest-Sphinx-Docs/)

diff --git a/tox.ini b/tox.ini
@@ -19,7 +19,7 @@ commands =
 allowlist_externals =
     bash
     make
-passenv = 
+passenv =
     CI CONDA_EXE
     GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION
     APP_WEBSERVER
@@ -55,7 +55,7 @@ commands = bash .ci/validate_test_tools.sh
 commands = bash .ci/check_controller.sh
 
 [testenv:check_indexes]
-commands = 
+commands =
     bash scripts/common_startup.sh
     bash manage_db.sh init
     bash check_model.sh
-Original file line number
+Diff line change
@@ Expand Up / @@ -3,6 +3,11 @@ History @@
     .. to_doc
+    ---------------------
+.5.0.dev0
+    ---------------------
     ---------------------
 .1.0.dev0
     ---------------------
@@ Expand Down @@