From cf656df57a6d4e1a9ad3c92a79f89b96d1c4523f Mon Sep 17 00:00:00 2001 From: Kent Pitman Date: Sat, 12 Aug 2023 04:12:13 -0400 Subject: [PATCH 1/5] First cut at fixing publication bugs. --- .github/workflows/main-publish.yml | 6 +++++- CHANGELOG.rst | 6 ++++++ pyproject.toml | 2 +- 3 files changed, 12 insertions(+), 2 deletions(-) diff --git a/.github/workflows/main-publish.yml b/.github/workflows/main-publish.yml index a6d8923..239e023 100644 --- a/.github/workflows/main-publish.yml +++ b/.github/workflows/main-publish.yml @@ -28,10 +28,14 @@ jobs: with: # For publication, we're not testing anything, so use latest allowable version of Python python-version: 3.9 + + - name: Build + run: | + make build + - name: Publish env: PYPI_USER: ${{ secrets.PYPI_USER }} PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }} run: | - make configure make publish-for-ga diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 95769c1..3ac314a 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -6,6 +6,12 @@ submitr Change Log ---------- +0.3.2 +===== + +* Fix auto-publish on pushing a tag. + + 0.3.1 ===== diff --git a/pyproject.toml b/pyproject.toml index e9daae9..38690a6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "submitr" -version = "0.3.1" +version = "0.3.1.1b0" # to become "0.3.2" description = "Support for uploading file submissions to SMAHT." # TODO: Update this email address when a more specific one is available for SMaHT. authors = ["4DN-DCIC Team "] From 8d8845588d62908dd454774036ec417feaacf3ea Mon Sep 17 00:00:00 2001 From: Kent Pitman Date: Sat, 12 Aug 2023 04:28:18 -0400 Subject: [PATCH 2/5] De-beta as submitr 0.3.2 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 38690a6..cd07bbf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "submitr" -version = "0.3.1.1b0" # to become "0.3.2" +version = "0.3.2" # "0.3.2" was tested successfully as "0.3.1.1b0" description = "Support for uploading file submissions to SMAHT." # TODO: Update this email address when a more specific one is available for SMaHT. authors = ["4DN-DCIC Team "] From 90de67fcababce495e7b8c3b09d4600dfbbec812 Mon Sep 17 00:00:00 2001 From: Kent Pitman Date: Sat, 12 Aug 2023 18:42:38 -0400 Subject: [PATCH 3/5] Disable scripts/publish per David's code review. --- scripts/{publish => publish.DISABLED} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename scripts/{publish => publish.DISABLED} (100%) diff --git a/scripts/publish b/scripts/publish.DISABLED similarity index 100% rename from scripts/publish rename to scripts/publish.DISABLED From 836fd3c43e06115bc80cb097d78d635a667a349e Mon Sep 17 00:00:00 2001 From: Kent Pitman Date: Sat, 12 Aug 2023 18:43:19 -0400 Subject: [PATCH 4/5] Opportunistic: Adjust the way some sections and subsections are presented to make things a bit more aesthetic. --- docs/source/submitr.rst | 23 +++++++++++------------ docs/source/submitr.scripts.rst | 11 ++++------- docs/source/submitr.tests.rst | 19 ++++++++----------- 3 files changed, 23 insertions(+), 30 deletions(-) diff --git a/docs/source/submitr.rst b/docs/source/submitr.rst index 4e02965..4648e6a 100644 --- a/docs/source/submitr.rst +++ b/docs/source/submitr.rst @@ -1,18 +1,6 @@ submitr package =============== -Subpackages ------------ - -.. toctree:: - :maxdepth: 4 - - submitr.scripts - submitr.tests - -Submodules ----------- - submitr.base module ------------------- @@ -44,3 +32,14 @@ submitr.utils module :members: :undoc-members: :show-inheritance: + +------------------------- + +submitr subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + submitr.scripts + submitr.tests diff --git a/docs/source/submitr.scripts.rst b/docs/source/submitr.scripts.rst index 53dd56a..75a2508 100644 --- a/docs/source/submitr.scripts.rst +++ b/docs/source/submitr.scripts.rst @@ -1,11 +1,8 @@ submitr.scripts package ============================ -Submodules ----------- - submitr.scripts.make\_sample\_fastq\_file module ------------------------------------------------------ +------------------------------------------------ .. automodule:: submitr.scripts.make_sample_fastq_file :members: @@ -13,7 +10,7 @@ submitr.scripts.make\_sample\_fastq\_file module :show-inheritance: submitr.scripts.resume\_uploads module -------------------------------------------- +-------------------------------------- .. automodule:: submitr.scripts.resume_uploads :members: @@ -21,7 +18,7 @@ submitr.scripts.resume\_uploads module :show-inheritance: submitr.scripts.submit\_metadata\_bundle module ----------------------------------------------------- +----------------------------------------------- .. automodule:: submitr.scripts.submit_metadata_bundle :members: @@ -29,7 +26,7 @@ submitr.scripts.submit\_metadata\_bundle module :show-inheritance: submitr.scripts.upload\_item\_data module ----------------------------------------------- +----------------------------------------- .. automodule:: submitr.scripts.upload_item_data :members: diff --git a/docs/source/submitr.tests.rst b/docs/source/submitr.tests.rst index 113eb47..1d4b843 100644 --- a/docs/source/submitr.tests.rst +++ b/docs/source/submitr.tests.rst @@ -1,11 +1,8 @@ submitr.tests package ========================== -Submodules ----------- - submitr.tests.test\_base module ------------------------------------- +------------------------------- .. automodule:: submitr.tests.test_base :members: @@ -13,7 +10,7 @@ submitr.tests.test\_base module :show-inheritance: submitr.tests.test\_exceptions module ------------------------------------------- +------------------------------------- .. automodule:: submitr.tests.test_exceptions :members: @@ -21,7 +18,7 @@ submitr.tests.test\_exceptions module :show-inheritance: submitr.tests.test\_make\_sample\_fastq\_file module ---------------------------------------------------------- +---------------------------------------------------- .. automodule:: submitr.tests.test_make_sample_fastq_file :members: @@ -29,7 +26,7 @@ submitr.tests.test\_make\_sample\_fastq\_file module :show-inheritance: submitr.tests.test\_resume\_uploads module ------------------------------------------------ +------------------------------------------ .. automodule:: submitr.tests.test_resume_uploads :members: @@ -37,7 +34,7 @@ submitr.tests.test\_resume\_uploads module :show-inheritance: submitr.tests.test\_submission module ------------------------------------------- +------------------------------------- .. automodule:: submitr.tests.test_submission :members: @@ -45,7 +42,7 @@ submitr.tests.test\_submission module :show-inheritance: submitr.tests.test\_submit\_metadata\_bundle module --------------------------------------------------------- +--------------------------------------------------- .. automodule:: submitr.tests.test_submit_metadata_bundle :members: @@ -53,7 +50,7 @@ submitr.tests.test\_submit\_metadata\_bundle module :show-inheritance: submitr.tests.test\_upload\_item\_data module --------------------------------------------------- +--------------------------------------------- .. automodule:: submitr.tests.test_upload_item_data :members: @@ -61,7 +58,7 @@ submitr.tests.test\_upload\_item\_data module :show-inheritance: submitr.tests.test\_utils module -------------------------------------- +-------------------------------- .. automodule:: submitr.tests.test_utils :members: From 099fcc15948d6c51146d384c4f587a69ce31940d Mon Sep 17 00:00:00 2001 From: Kent Pitman Date: Sat, 12 Aug 2023 18:50:28 -0400 Subject: [PATCH 5/5] Fill out CHANGELOG. --- CHANGELOG.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 3ac314a..79ea27e 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -10,6 +10,8 @@ Change Log ===== * Fix auto-publish on pushing a tag. +* Disabled ``scripts/publish`` since we're using functionality from ``dcicutils.scripts`` now. +* Adjusted headings to present with better indentation and better recursive header presentation. 0.3.1