From c66a969a678a8cde4579f46c9c8ee862bca592dd Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Wed, 25 Sep 2024 22:49:06 +0100 Subject: [PATCH 1/4] Update CITATION.cff --- CITATION.cff | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 795f811fc..a4575b565 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -28,9 +28,15 @@ authors: - given-names: "David" family-names: "Dotson" orcid: "https://orcid.org/0000-0001-5879-2942" +- given-names: Joshua T. + family-names: Horton + orcid: 'https://orcid.org/0000-0001-8694-7200' +- given-names: Matthew + family-names: Thompson + orcid: 'https://orcid.org/0000-0002-1460-3983' title: "The Open Free Energy library" -version: 1.0 -date-released: 2024-04-19 +version: 1.1.0 +date-released: 2024-09-25 url: "https://openfree.energy/" repository-code: "https://github.com/openfreeEnergy/openfe" doi: 10.5281/zenodo.8344247 From 7db0c4147ffc8279793e8a667402f406a4496856 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Wed, 25 Sep 2024 22:53:08 +0100 Subject: [PATCH 2/4] Updated CHANGELOG for 1.1.0 --- docs/CHANGELOG.rst | 35 +++++++++++++++++++++++++++++++++++ news/noncubic_solvent.rst | 25 ------------------------- news/pr_896.rst | 25 ------------------------- news/pr_930.rst | 23 ----------------------- news/pr_937.rst | 32 -------------------------------- news/pymbar_duecredit.rst | 24 ------------------------ 6 files changed, 35 insertions(+), 129 deletions(-) delete mode 100644 news/noncubic_solvent.rst delete mode 100644 news/pr_896.rst delete mode 100644 news/pr_930.rst delete mode 100644 news/pr_937.rst delete mode 100644 news/pymbar_duecredit.rst diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst index 59bd94d6c..243fee470 100644 --- a/docs/CHANGELOG.rst +++ b/docs/CHANGELOG.rst @@ -4,6 +4,41 @@ Changelog .. current developments +v1.1.0 +==================== + +**Added:** + +* Extended system solvation tooling, including support for; non-cubic boxes, + explicitly defining the number of waters added, the box vectors, and box size + as supported by `Modeller.addSolvent` in OpenMM 8.0 and above. + +**Changed:** + +* Improved documentation of the OpenMMSolvationSettings. +* The `PersesAtomMapper` now uses openff.units inline with the rest of the package. +* Structural analysis data is no longer written to `structural_analysis.json` + but rather a 32bit numpy compressed file named `structural_analysis.npz` + (PR #937). +* Structural analysis array data is no longer directly returned in the + RelativeHybridTopologyProtocol result dictionary. Instead it should + be accessed from the serialized NPZ file `structural_analysis.npz`. + The `structural_analysis` key now contains a path to the NPZ file, + if the structural analysis did not fail (the `structural_analysis_error` + key will instead be present on failure) (PR #937). +* Add duecredit citations for pymbar when calling + `openfe.protocols.openmm_utils.multistate_analysis`. + +**Fixed:** + +* 2D RMSD plotting now allows for fewer than 5 states (PR #896). +* 2D RMSD plotting no longer draws empty axes when + the number of states - 1 is not divisible by 4 (PR #896). +* The RelativeHybridTopologyProtocol result unit is now much smaller, + due to the removal of structural analysis data (PR #937). + + + v1.0.1 ==================== diff --git a/news/noncubic_solvent.rst b/news/noncubic_solvent.rst deleted file mode 100644 index 64320ba6d..000000000 --- a/news/noncubic_solvent.rst +++ /dev/null @@ -1,25 +0,0 @@ -**Added:** - -* Extended system solvation tooling, including support for; non-cubic boxes, - explicitly defining the number of waters added, the box vectors, and box size - as supported by `Modeller.addSolvent` in OpenMM 8.0 and above. - -**Changed:** - -* Improved documentation of the OpenMMSolvationSettings. - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/pr_896.rst b/news/pr_896.rst deleted file mode 100644 index 43101e839..000000000 --- a/news/pr_896.rst +++ /dev/null @@ -1,25 +0,0 @@ -**Added:** - -* - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* 2D RMSD plotting now allows for fewer than 5 states (PR #896). -* 2D RMSD plotting no longer draws empty axes when - the number of states - 1 is not divisible by 4 (PR #896). - -**Security:** - -* diff --git a/news/pr_930.rst b/news/pr_930.rst deleted file mode 100644 index 4aa0aa880..000000000 --- a/news/pr_930.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* - -**Changed:** - -* The `PersesAtomMapper` now uses openff.units inline with the rest of the package. - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/pr_937.rst b/news/pr_937.rst deleted file mode 100644 index 3b4c61b79..000000000 --- a/news/pr_937.rst +++ /dev/null @@ -1,32 +0,0 @@ -**Added:** - -* - -**Changed:** - -* Structural analysis data is no longer written to `structural_analysis.json` - but rather a 32bit numpy compressed file named `structural_analysis.npz` - (PR #937). -* Structural analysis array data is no longer directly returned in the - RelativeHybridTopologyProtocol result dictionary. Instead it should - be accessed from the serialized NPZ file `structural_analysis.npz`. - The `structural_analysis` key now contains a path to the NPZ file, - if the structural analysis did not fail (the `structural_analysis_error` - key will instead be present on failure) (PR #937). - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* The RelativeHybridTopologyProtocol result unit is now much smaller, - due to the removal of structural analysis data (PR #937). - -**Security:** - -* diff --git a/news/pymbar_duecredit.rst b/news/pymbar_duecredit.rst deleted file mode 100644 index 5cfa09038..000000000 --- a/news/pymbar_duecredit.rst +++ /dev/null @@ -1,24 +0,0 @@ -**Added:** - -* - -**Changed:** - -* Add duecredit citations for pymbar when calling - `openfe.protocols.openmm_utils.multistate_analysis`. - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* From 1aaa37f325b3cf8004cabb14116ad29b193857b0 Mon Sep 17 00:00:00 2001 From: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Date: Wed, 25 Sep 2024 15:10:59 -0700 Subject: [PATCH 3/4] pin micromamba version --- .github/workflows/ci.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index f6041fafc..d7bd615b6 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -73,6 +73,7 @@ jobs: - name: "Setup Micromamba" uses: mamba-org/setup-micromamba@v1 with: + micromamba-version: '1.5.6-0' micromamba-binary-path: ~/.local/bin/micromamba environment-file: environment.yml environment-name: openfe_env From 1672985f75f7d557dec61ffdbc0eb38e3a51164f Mon Sep 17 00:00:00 2001 From: IAlibay Date: Wed, 25 Sep 2024 23:31:51 +0100 Subject: [PATCH 4/4] All the pins --- .github/workflows/conda_cron.yaml | 1 + .github/workflows/gpu-runner.yaml | 1 + .github/workflows/installer.yaml | 1 + .github/workflows/mypy.yaml | 1 + .github/workflows/package-tests.yaml | 1 + 5 files changed, 5 insertions(+) diff --git a/.github/workflows/conda_cron.yaml b/.github/workflows/conda_cron.yaml index 95b3b39dc..0aa542198 100644 --- a/.github/workflows/conda_cron.yaml +++ b/.github/workflows/conda_cron.yaml @@ -34,6 +34,7 @@ jobs: - name: Setup Micromamba uses: mamba-org/setup-micromamba@v1 with: + micromamba-version: '1.5.6-0' micromamba-binary-path: ~/.local/bin/micromamba environment-name: openfe create-args: >- diff --git a/.github/workflows/gpu-runner.yaml b/.github/workflows/gpu-runner.yaml index f93a3dfae..b9d14c805 100644 --- a/.github/workflows/gpu-runner.yaml +++ b/.github/workflows/gpu-runner.yaml @@ -55,6 +55,7 @@ jobs: - name: "Setup Micromamba" uses: mamba-org/setup-micromamba@v1 with: + micromamba-version: '1.5.6-0' environment-file: environment.yml environment-name: openfe_env condarc: | diff --git a/.github/workflows/installer.yaml b/.github/workflows/installer.yaml index ace15afdb..4fac5c433 100644 --- a/.github/workflows/installer.yaml +++ b/.github/workflows/installer.yaml @@ -37,6 +37,7 @@ jobs: - name: Install constructor environment with Micromamba uses: mamba-org/setup-micromamba@v1 with: + micromamba-version: '1.5.6-0' micromamba-binary-path: ~/.local/bin/micromamba environment-name: installer create-args: >- diff --git a/.github/workflows/mypy.yaml b/.github/workflows/mypy.yaml index e83beb55d..7a7025a62 100644 --- a/.github/workflows/mypy.yaml +++ b/.github/workflows/mypy.yaml @@ -28,6 +28,7 @@ jobs: - name: "Setup Micromamba" uses: mamba-org/setup-micromamba@v1 with: + micromamba-version: '1.5.6-0' environment-file: environment.yml environment-name: openfe_env cache-environment: true diff --git a/.github/workflows/package-tests.yaml b/.github/workflows/package-tests.yaml index c56f40c3b..d3dc68473 100644 --- a/.github/workflows/package-tests.yaml +++ b/.github/workflows/package-tests.yaml @@ -22,6 +22,7 @@ jobs: - name: "Setup Micromamba" uses: mamba-org/setup-micromamba@v1 with: + micromamba-version: '1.5.6-0' environment-file: environment.yml environment-name: openfe_env cache-environment: true