From c0e945b802a4d1b7765bd0c6d498ba875f652f01 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Thu, 7 Nov 2024 13:40:12 -0700 Subject: [PATCH 1/8] Added release prep PR template --- .github/PULL_REQUEST_TEMPLATE/release-prep.md | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 .github/PULL_REQUEST_TEMPLATE/release-prep.md diff --git a/.github/PULL_REQUEST_TEMPLATE/release-prep.md b/.github/PULL_REQUEST_TEMPLATE/release-prep.md new file mode 100644 index 00000000..2720b04d --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE/release-prep.md @@ -0,0 +1,10 @@ +--- +name: Release preparation +about: Prepare a new release for this package +title: 'Release : ' +labels: 'release-prep' +assignees: '' + +--- + + From 7efa354079db709a06c12311cbe8326904d8cdc1 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Thu, 7 Nov 2024 14:18:37 -0700 Subject: [PATCH 2/8] Added PR template content --- .github/PULL_REQUEST_TEMPLATE/release-prep.md | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/.github/PULL_REQUEST_TEMPLATE/release-prep.md b/.github/PULL_REQUEST_TEMPLATE/release-prep.md index 2720b04d..dbc73ceb 100644 --- a/.github/PULL_REQUEST_TEMPLATE/release-prep.md +++ b/.github/PULL_REQUEST_TEMPLATE/release-prep.md @@ -7,4 +7,16 @@ assignees: '' --- +To create a new release, please do the following: +- [ ] make any changes to the repo needed to accommodate the release +- [ ] run `rever` to generate the `CHANGELOG` entry from `news` items +- [ ] merge this PR into `main` + + +After you have merged this PR, please also: + +- [ ] create a release here in GitHub, including generating detailed release notes + - [ ] in the summary release notes, also link to the `CHANGELOG` entry for this release in the `gufe` docs +- [ ] await automated PR on `conda-forge` `gufe-feedstock` + - [ ] review and merge From cb132e1f32c1e34d8c2bba04b176bc33f2760d22 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Thu, 7 Nov 2024 14:28:15 -0700 Subject: [PATCH 3/8] Added some additional detail to PR template --- .github/PULL_REQUEST_TEMPLATE/release-prep.md | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/.github/PULL_REQUEST_TEMPLATE/release-prep.md b/.github/PULL_REQUEST_TEMPLATE/release-prep.md index dbc73ceb..005bd693 100644 --- a/.github/PULL_REQUEST_TEMPLATE/release-prep.md +++ b/.github/PULL_REQUEST_TEMPLATE/release-prep.md @@ -8,15 +8,14 @@ assignees: '' --- To create a new release, please do the following: - - [ ] make any changes to the repo needed to accommodate the release -- [ ] run `rever` to generate the `CHANGELOG` entry from `news` items + - [ ] check `environment.yml` for any updates needed; create any issues needed to update versions in next release cycle +- [ ] run [`rever`](https://regro.github.io/rever-docs/index.html#rever-releaser-of-versions) to generate the `CHANGELOG` entry from `news` items - [ ] merge this PR into `main` After you have merged this PR, please also: - - [ ] create a release here in GitHub, including generating detailed release notes - [ ] in the summary release notes, also link to the `CHANGELOG` entry for this release in the `gufe` docs -- [ ] await automated PR on `conda-forge` `gufe-feedstock` +- [ ] await automated PR on `conda-forge` [`gufe-feedstock` `meta.yaml`](https://github.com/conda-forge/gufe-feedstock/blob/main/recipe/meta.yaml) - [ ] review and merge From 9edbd54d60d24b17d882e47e0818506e0419175b Mon Sep 17 00:00:00 2001 From: David Dotson Date: Thu, 7 Nov 2024 14:29:21 -0700 Subject: [PATCH 4/8] Updated CHANGELOG for 1.1.0 --- docs/CHANGELOG.rst | 27 +++++++++++++++++++++++++++ news/add_rever.rst | 23 ----------------------- news/backfill_new.rst | 31 ------------------------------- news/graphml_annotations.rst | 23 ----------------------- 4 files changed, 27 insertions(+), 77 deletions(-) delete mode 100644 news/add_rever.rst delete mode 100644 news/backfill_new.rst delete mode 100644 news/graphml_annotations.rst diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst index d29a6783..a50a0eda 100644 --- a/docs/CHANGELOG.rst +++ b/docs/CHANGELOG.rst @@ -3,3 +3,30 @@ gufe Change Log =============== .. current developments + +v1.1.0 +==================== + +**Added:** + +* use rever to manage changelog +* KeyedChain GufeTokenizable representation was added, allowing + GUFE objects to be deduplicated when serializing GufeTokenizables + (PR #286). +* Added `to_json` and `from_json` convenience methods to GufeTokenizables + to more easily convert to a JSON keyed chain representation (PR #368). + +**Changed:** + +* Minimum Python version has been raised to v3.10 (PR #340) + +**Fixed:** + +* Fixed an issue where partial charges were not being read from rdkit + Molecules where atom level properties were not set. This occured + mainly when reading from an SDF file with partial charge tags (PR #312). +* Fixed an issue where ProtocolDAG DAG order & keys were unstable / + non-deterministic between processes under some circumstances (PR #315). +* Fixed a bug where edge annotations were lost when converting a ``LigandNetwork`` to graphml, all JSON codec types are now supported. + + diff --git a/news/add_rever.rst b/news/add_rever.rst deleted file mode 100644 index 60a6f406..00000000 --- a/news/add_rever.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* use rever to manage changelog - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/backfill_new.rst b/news/backfill_new.rst deleted file mode 100644 index 61333c02..00000000 --- a/news/backfill_new.rst +++ /dev/null @@ -1,31 +0,0 @@ -**Added:** - -* KeyedChain GufeTokenizable representation was added, allowing - GUFE objects to be deduplicated when serializing GufeTokenizables - (PR #286). -* Added `to_json` and `from_json` convenience methods to GufeTokenizables - to more easily convert to a JSON keyed chain representation (PR #368). - -**Changed:** - -* Minimum Python version has been raised to v3.10 (PR #340) - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* Fixed an issue where partial charges were not being read from rdkit - Molecules where atom level properties were not set. This occured - mainly when reading from an SDF file with partial charge tags (PR #312). -* Fixed an issue where ProtocolDAG DAG order & keys were unstable / - non-deterministic between processes under some circumstances (PR #315). - -**Security:** - -* diff --git a/news/graphml_annotations.rst b/news/graphml_annotations.rst deleted file mode 100644 index b142b305..00000000 --- a/news/graphml_annotations.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* Fixed a bug where edge annotations were lost when converting a ``LigandNetwork`` to graphml, all JSON codec types are now supported. - -**Security:** - -* From ab5a524755fbb06c4aa75d4ec4811ae3b144cf09 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Thu, 7 Nov 2024 14:31:30 -0700 Subject: [PATCH 5/8] added rever command to PR template --- .github/PULL_REQUEST_TEMPLATE/release-prep.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/PULL_REQUEST_TEMPLATE/release-prep.md b/.github/PULL_REQUEST_TEMPLATE/release-prep.md index 005bd693..2295e75a 100644 --- a/.github/PULL_REQUEST_TEMPLATE/release-prep.md +++ b/.github/PULL_REQUEST_TEMPLATE/release-prep.md @@ -10,7 +10,7 @@ assignees: '' To create a new release, please do the following: - [ ] make any changes to the repo needed to accommodate the release - [ ] check `environment.yml` for any updates needed; create any issues needed to update versions in next release cycle -- [ ] run [`rever`](https://regro.github.io/rever-docs/index.html#rever-releaser-of-versions) to generate the `CHANGELOG` entry from `news` items +- [ ] run [`rever`](https://regro.github.io/rever-docs/index.html#rever-releaser-of-versions) to generate the `CHANGELOG` entry from `news` items: `rever ` - [ ] merge this PR into `main` From 5bce6f22527defd95e175210172a31f0503e3fde Mon Sep 17 00:00:00 2001 From: David Dotson Date: Thu, 7 Nov 2024 14:33:04 -0700 Subject: [PATCH 6/8] inspect CHANGELOG --- .github/PULL_REQUEST_TEMPLATE/release-prep.md | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/PULL_REQUEST_TEMPLATE/release-prep.md b/.github/PULL_REQUEST_TEMPLATE/release-prep.md index 2295e75a..7d30c0f3 100644 --- a/.github/PULL_REQUEST_TEMPLATE/release-prep.md +++ b/.github/PULL_REQUEST_TEMPLATE/release-prep.md @@ -11,6 +11,7 @@ To create a new release, please do the following: - [ ] make any changes to the repo needed to accommodate the release - [ ] check `environment.yml` for any updates needed; create any issues needed to update versions in next release cycle - [ ] run [`rever`](https://regro.github.io/rever-docs/index.html#rever-releaser-of-versions) to generate the `CHANGELOG` entry from `news` items: `rever ` + - inspect `CHANGELOG`, adjust as necessary - [ ] merge this PR into `main` From 6a1637727cae1945d3cc5a1ea446dc15604a1fe9 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Thu, 7 Nov 2024 14:39:28 -0700 Subject: [PATCH 7/8] Updated classifiers in pyproject.toml --- pyproject.toml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index e54bad84..be1533bf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,11 +12,10 @@ readme = "README.md" authors = [{name = "The OpenFE developers", email = "openfe@omsf.io"}] license = {text = "MIT"} classifiers = [ - "Development Status :: 1 - Planning", + "Development Status :: 5 - Production/Stable" "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Operating System :: POSIX", - "Operating System :: Microsoft :: Windows", "Programming Language :: Python :: 3", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Scientific/Engineering :: Chemistry", From 0d3783d7541a31d50e52582e350599fafb1d0bbc Mon Sep 17 00:00:00 2001 From: David Dotson Date: Thu, 7 Nov 2024 14:46:37 -0700 Subject: [PATCH 8/8] Fixed comma --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index be1533bf..d68b3488 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ readme = "README.md" authors = [{name = "The OpenFE developers", email = "openfe@omsf.io"}] license = {text = "MIT"} classifiers = [ - "Development Status :: 5 - Production/Stable" + "Development Status :: 5 - Production/Stable", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Operating System :: POSIX",