From f8ecbe459f16b7e2f779761aca20a4fd616723d6 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Wed, 28 Jun 2023 23:22:30 -0700 Subject: [PATCH 1/9] Updated dependencies in conda envs, both testing and deployment Trying out Python 3.10, also using latest releases of `gufe` (0.9.0) and `openfe` (0.10.1) for deployment envs. --- devtools/conda-envs/alchemiscale-client.yml | 6 +++--- devtools/conda-envs/alchemiscale-compute.yml | 6 +++--- devtools/conda-envs/alchemiscale-server.yml | 6 +++--- devtools/conda-envs/docs.yml | 4 ++-- devtools/conda-envs/test.yml | 4 ++-- 5 files changed, 13 insertions(+), 13 deletions(-) diff --git a/devtools/conda-envs/alchemiscale-client.yml b/devtools/conda-envs/alchemiscale-client.yml index 92394fec..40d0a8eb 100644 --- a/devtools/conda-envs/alchemiscale-client.yml +++ b/devtools/conda-envs/alchemiscale-client.yml @@ -5,11 +5,11 @@ channels: - openeye dependencies: - pip - - python =3.9 + - python =3.10 # alchemiscale dependencies - - gufe=0.7.3 - - openfe=0.7.4 + - gufe=0.9.0 + - openfe=0.10.1 - requests - click diff --git a/devtools/conda-envs/alchemiscale-compute.yml b/devtools/conda-envs/alchemiscale-compute.yml index 1d19eed5..c0c7f5b8 100644 --- a/devtools/conda-envs/alchemiscale-compute.yml +++ b/devtools/conda-envs/alchemiscale-compute.yml @@ -4,12 +4,12 @@ channels: - openeye dependencies: - pip - - python =3.9 + - python =3.10 - cudatoolkit <=11.7 # many actual compute resources are not yet compatible with cudatoolkit >=11.8 # alchemiscale dependencies - - gufe=0.7.3 - - openfe=0.7.4 + - gufe=0.9.0 + - openfe=0.10.1 - requests - click diff --git a/devtools/conda-envs/alchemiscale-server.yml b/devtools/conda-envs/alchemiscale-server.yml index 8f41c449..dfc107db 100644 --- a/devtools/conda-envs/alchemiscale-server.yml +++ b/devtools/conda-envs/alchemiscale-server.yml @@ -5,11 +5,11 @@ channels: - openeye dependencies: - pip - - python =3.9 + - python =3.10 # alchemiscale dependencies - - gufe=0.7.3 - - openfe=0.7.4 + - gufe=0.9.0 + - openfe=0.10.1 - requests - click diff --git a/devtools/conda-envs/docs.yml b/devtools/conda-envs/docs.yml index 0e7263ab..90eb96bc 100644 --- a/devtools/conda-envs/docs.yml +++ b/devtools/conda-envs/docs.yml @@ -5,10 +5,10 @@ channels: - openeye dependencies: - pip - - python =3.9 + - python =3.10 # gufe dependencies - - numpy<1.24 # https://github.com/numba/numba/issues/8615#issuecomment-1360792615 + - numpy - networkx - rdkit - pydantic diff --git a/devtools/conda-envs/test.yml b/devtools/conda-envs/test.yml index aac7b47c..a58abd39 100644 --- a/devtools/conda-envs/test.yml +++ b/devtools/conda-envs/test.yml @@ -5,10 +5,10 @@ channels: - openeye dependencies: - pip - - python =3.9 + - python =3.10 # gufe dependencies - - numpy<1.24 # https://github.com/numba/numba/issues/8615#issuecomment-1360792615 + - numpy - networkx - rdkit - pydantic From 8b7ecd192b58e075262f3c7acbc87f420a964702 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Wed, 28 Jun 2023 23:52:40 -0700 Subject: [PATCH 2/9] Update CI python to 3.10 --- .github/workflows/ci-integration.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-integration.yml b/.github/workflows/ci-integration.yml index 86151f40..1ef49bae 100644 --- a/.github/workflows/ci-integration.yml +++ b/.github/workflows/ci-integration.yml @@ -27,7 +27,7 @@ jobs: matrix: os: ['ubuntu'] python-version: - - 3.9 + - 3.10 env: OE_LICENSE: ${{ github.workspace }}/oe_license.txt From 08b2af3cc06ed095ee1cbea0d28548add5523923 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Wed, 28 Jun 2023 23:55:57 -0700 Subject: [PATCH 3/9] Yaml need quotes for 3.10 to not become 3.1 --- .github/workflows/ci-integration.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-integration.yml b/.github/workflows/ci-integration.yml index 1ef49bae..5c0bec81 100644 --- a/.github/workflows/ci-integration.yml +++ b/.github/workflows/ci-integration.yml @@ -27,7 +27,7 @@ jobs: matrix: os: ['ubuntu'] python-version: - - 3.10 + - "3.10" env: OE_LICENSE: ${{ github.workspace }}/oe_license.txt From 35ce46ea5f164763b07d651fc215bc9a9ff9db97 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Thu, 29 Jun 2023 00:15:52 -0700 Subject: [PATCH 4/9] Update Python version of docs build :/ --- .github/workflows/docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index ebb5e825..05f493c6 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -25,7 +25,7 @@ jobs: with: auto-update-conda: true use-mamba: true - python-version: 3.9 + python-version: "3.10" miniforge-variant: Mambaforge environment-file: devtools/conda-envs/docs.yml activate-environment: alchemiscale-docs From 6ef2a1e024c7ad3dd04e786e87afdcf505dfdc67 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Thu, 29 Jun 2023 00:17:43 -0700 Subject: [PATCH 5/9] Add httpx to client env --- devtools/conda-envs/alchemiscale-client.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/devtools/conda-envs/alchemiscale-client.yml b/devtools/conda-envs/alchemiscale-client.yml index 4de613cd..85b2cd42 100644 --- a/devtools/conda-envs/alchemiscale-client.yml +++ b/devtools/conda-envs/alchemiscale-client.yml @@ -12,6 +12,7 @@ dependencies: - openfe=0.10.1 - requests - click + - httpx ## user client printing - rich From 449ef9d60701266ad78d913f3ca7deeb1ac36c09 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Thu, 29 Jun 2023 00:32:02 -0700 Subject: [PATCH 6/9] Small color changes for readability --- alchemiscale/interface/client.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/alchemiscale/interface/client.py b/alchemiscale/interface/client.py index 7800982c..35604f6b 100644 --- a/alchemiscale/interface/client.py +++ b/alchemiscale/interface/client.py @@ -464,8 +464,8 @@ def _visualize_status(self, status_counts, status_object): table.add_row("complete", f"{status_counts.get('complete', 0)}", style="green") table.add_row("running", f"{status_counts.get('running', 0)}", style="orange3") - table.add_row("waiting", f"{status_counts.get('waiting', 0)}", style="blue") - table.add_row("error", f"{status_counts.get('error', 0)}", style="red") + table.add_row("waiting", f"{status_counts.get('waiting', 0)}", style="#1793d0") + table.add_row("error", f"{status_counts.get('error', 0)}", style="#ff073a") table.add_row("invalid", f"{status_counts.get('invalid', 0)}", style="magenta1") table.add_row("deleted", f"{status_counts.get('deleted', 0)}", style="purple") From 0a94c815b6cd1bf7ad51bab8b05a699cd3b0b927 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Thu, 29 Jun 2023 01:08:18 -0700 Subject: [PATCH 7/9] Set prod envs to use v0.1.3 once cut --- devtools/conda-envs/alchemiscale-client.yml | 2 +- devtools/conda-envs/alchemiscale-compute.yml | 2 +- devtools/conda-envs/alchemiscale-server.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/devtools/conda-envs/alchemiscale-client.yml b/devtools/conda-envs/alchemiscale-client.yml index 85b2cd42..e8ab8f2d 100644 --- a/devtools/conda-envs/alchemiscale-client.yml +++ b/devtools/conda-envs/alchemiscale-client.yml @@ -28,5 +28,5 @@ dependencies: - pip: - nest_asyncio - - git+https://github.com/openforcefield/alchemiscale.git@v0.1.2 + - git+https://github.com/openforcefield/alchemiscale.git@v0.1.3 - git+https://github.com/choderalab/perses.git@protocol-neqcyc diff --git a/devtools/conda-envs/alchemiscale-compute.yml b/devtools/conda-envs/alchemiscale-compute.yml index 1e9907a5..339f2dde 100644 --- a/devtools/conda-envs/alchemiscale-compute.yml +++ b/devtools/conda-envs/alchemiscale-compute.yml @@ -24,5 +24,5 @@ dependencies: - pymbar >=3.0.6,<4 - pip: - - git+https://github.com/openforcefield/alchemiscale.git@v0.1.2 + - git+https://github.com/openforcefield/alchemiscale.git@v0.1.3 - git+https://github.com/choderalab/perses.git@protocol-neqcyc diff --git a/devtools/conda-envs/alchemiscale-server.yml b/devtools/conda-envs/alchemiscale-server.yml index dfc107db..28bc8f74 100644 --- a/devtools/conda-envs/alchemiscale-server.yml +++ b/devtools/conda-envs/alchemiscale-server.yml @@ -42,5 +42,5 @@ dependencies: - pymbar >=3.0.6,<4 - pip: - - git+https://github.com/openforcefield/alchemiscale.git@v0.1.2 + - git+https://github.com/openforcefield/alchemiscale.git@v0.1.3 - git+https://github.com/choderalab/perses.git@protocol-neqcyc From ab4e2a45b740a395713674890c1133131dfb121c Mon Sep 17 00:00:00 2001 From: David Dotson Date: Thu, 29 Jun 2023 08:49:12 -0700 Subject: [PATCH 8/9] Added build matrix to CI, python 3.9; dropped Python pin in test and docs conda envs --- .github/workflows/ci-integration.yml | 1 + devtools/conda-envs/docs.yml | 1 - devtools/conda-envs/test.yml | 1 - 3 files changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/ci-integration.yml b/.github/workflows/ci-integration.yml index 5c0bec81..e9c4cacb 100644 --- a/.github/workflows/ci-integration.yml +++ b/.github/workflows/ci-integration.yml @@ -27,6 +27,7 @@ jobs: matrix: os: ['ubuntu'] python-version: + - "3.9" - "3.10" env: OE_LICENSE: ${{ github.workspace }}/oe_license.txt diff --git a/devtools/conda-envs/docs.yml b/devtools/conda-envs/docs.yml index 90eb96bc..c80500a0 100644 --- a/devtools/conda-envs/docs.yml +++ b/devtools/conda-envs/docs.yml @@ -5,7 +5,6 @@ channels: - openeye dependencies: - pip - - python =3.10 # gufe dependencies - numpy diff --git a/devtools/conda-envs/test.yml b/devtools/conda-envs/test.yml index a58abd39..ca171219 100644 --- a/devtools/conda-envs/test.yml +++ b/devtools/conda-envs/test.yml @@ -5,7 +5,6 @@ channels: - openeye dependencies: - pip - - python =3.10 # gufe dependencies - numpy From 1d60770c1246fb529886d3f7b8e47bf4151ae409 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Thu, 29 Jun 2023 10:06:42 -0700 Subject: [PATCH 9/9] Putting numpy pin for tests and docs back due to failure on Python 3.9 Latest numpy doesn't cause problems on 3.10. --- devtools/conda-envs/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/devtools/conda-envs/test.yml b/devtools/conda-envs/test.yml index ca171219..8137dd8d 100644 --- a/devtools/conda-envs/test.yml +++ b/devtools/conda-envs/test.yml @@ -7,7 +7,7 @@ dependencies: - pip # gufe dependencies - - numpy + - numpy<1.24 # https://github.com/numba/numba/issues/8615#issuecomment-1360792615 - networkx - rdkit - pydantic