From 6db4f8eda91d794d854c36f001c15d7473414d98 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Mon, 22 Jul 2024 23:47:48 -0700 Subject: [PATCH 01/18] Update prod envs to use Python 3.11 --- .github/workflows/ci-integration.yml | 2 +- devtools/conda-envs/alchemiscale-client.yml | 19 ++++--------------- devtools/conda-envs/alchemiscale-compute.yml | 15 ++------------- devtools/conda-envs/alchemiscale-server.yml | 15 ++------------- 4 files changed, 9 insertions(+), 42 deletions(-) diff --git a/.github/workflows/ci-integration.yml b/.github/workflows/ci-integration.yml index 36e1d380..773affd0 100644 --- a/.github/workflows/ci-integration.yml +++ b/.github/workflows/ci-integration.yml @@ -27,8 +27,8 @@ jobs: matrix: os: ['ubuntu'] python-version: - - "3.9" - "3.10" + - "3.11" steps: - uses: actions/checkout@v2 diff --git a/devtools/conda-envs/alchemiscale-client.yml b/devtools/conda-envs/alchemiscale-client.yml index 6f583986..2c2529c3 100644 --- a/devtools/conda-envs/alchemiscale-client.yml +++ b/devtools/conda-envs/alchemiscale-client.yml @@ -2,15 +2,14 @@ name: alchemiscale-client channels: - jaimergp/label/unsupported-cudatoolkit-shim - conda-forge - - openeye dependencies: - pip - - python =3.10 + - python =3.11 # alchemiscale dependencies - - gufe=0.9.5 - - openfe=0.14.0 + - gufe=1.0.0 + - openfe=1.0.1 - openmmforcefields>=0.12.0 - requests - click @@ -20,17 +19,7 @@ dependencies: ## user client printing - rich - # perses dependencies - - openeye-toolkits - - openmoltools - - cloudpathlib - - dask - - distributed - - numba - - pymbar >=3.0.6,<4 - - pip: - nest_asyncio - async_lru - - git+https://github.com/openforcefield/alchemiscale.git@v0.4.0 - - git+https://github.com/choderalab/perses.git@protocol-neqcyc + - git+https://github.com/openforcefield/alchemiscale.git@v0.5.0-beta.1 diff --git a/devtools/conda-envs/alchemiscale-compute.yml b/devtools/conda-envs/alchemiscale-compute.yml index 56b21cef..2a39e34e 100644 --- a/devtools/conda-envs/alchemiscale-compute.yml +++ b/devtools/conda-envs/alchemiscale-compute.yml @@ -1,11 +1,10 @@ name: alchemiscale-compute channels: - conda-forge - - openeye dependencies: - pip - - python =3.10 + - python =3.11 - cudatoolkit <=11.7 # many actual compute resources are not yet compatible with cudatoolkit >=11.8 # alchemiscale dependencies @@ -17,16 +16,6 @@ dependencies: - httpx - pydantic<2.0 - # perses dependencies - - openeye-toolkits - - openmoltools - - cloudpathlib - - dask - - distributed - - numba - - pymbar >=3.0.6,<4 - - pip: - async_lru - - git+https://github.com/openforcefield/alchemiscale.git@v0.4.0 - - git+https://github.com/choderalab/perses.git@protocol-neqcyc + - git+https://github.com/openforcefield/alchemiscale.git@v0.5.0 diff --git a/devtools/conda-envs/alchemiscale-server.yml b/devtools/conda-envs/alchemiscale-server.yml index f8909d40..202c5f84 100644 --- a/devtools/conda-envs/alchemiscale-server.yml +++ b/devtools/conda-envs/alchemiscale-server.yml @@ -2,11 +2,10 @@ name: alchemiscale-server channels: - jaimergp/label/unsupported-cudatoolkit-shim - conda-forge - - openeye dependencies: - pip - - python =3.10 + - python =3.11 # alchemiscale dependencies - gufe=0.9.5 @@ -37,16 +36,6 @@ dependencies: - httpx - cryptography - # perses dependencies - - openeye-toolkits - - openmoltools - - cloudpathlib - - dask - - distributed - - numba - - pymbar >=3.0.6,<4 - - pip: - async_lru - - git+https://github.com/openforcefield/alchemiscale.git@v0.4.0 - - git+https://github.com/choderalab/perses.git@protocol-neqcyc + - git+https://github.com/openforcefield/alchemiscale.git@v0.5.0-beta.1 From ecd8dad5631fa2827d781cc3c852ad1a68933cb1 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Mon, 22 Jul 2024 23:51:47 -0700 Subject: [PATCH 02/18] Update all envs to use gufe 1.0.0, openfe 1.0.1 --- devtools/conda-envs/alchemiscale-compute.yml | 6 +++--- devtools/conda-envs/alchemiscale-server.yml | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/devtools/conda-envs/alchemiscale-compute.yml b/devtools/conda-envs/alchemiscale-compute.yml index 2a39e34e..262ef7d0 100644 --- a/devtools/conda-envs/alchemiscale-compute.yml +++ b/devtools/conda-envs/alchemiscale-compute.yml @@ -8,8 +8,8 @@ dependencies: - cudatoolkit <=11.7 # many actual compute resources are not yet compatible with cudatoolkit >=11.8 # alchemiscale dependencies - - gufe=0.9.5 - - openfe=0.14.0 + - gufe=1.0.0 + - openfe=1.0.1 - openmmforcefields>=0.12.0 - requests - click @@ -18,4 +18,4 @@ dependencies: - pip: - async_lru - - git+https://github.com/openforcefield/alchemiscale.git@v0.5.0 + - git+https://github.com/openforcefield/alchemiscale.git@v0.5.0-beta.1 diff --git a/devtools/conda-envs/alchemiscale-server.yml b/devtools/conda-envs/alchemiscale-server.yml index 202c5f84..b89db17b 100644 --- a/devtools/conda-envs/alchemiscale-server.yml +++ b/devtools/conda-envs/alchemiscale-server.yml @@ -8,8 +8,8 @@ dependencies: - python =3.11 # alchemiscale dependencies - - gufe=0.9.5 - - openfe=0.14.0 + - gufe=1.0.0 + - openfe=1.0.1 - openmmforcefields>=0.12.0 - requests From 86ec725849a7d039f27bdf24a8b6a553152974cd Mon Sep 17 00:00:00 2001 From: David Dotson Date: Tue, 23 Jul 2024 09:21:44 -0700 Subject: [PATCH 03/18] Add Python 3.12 to CI --- .github/workflows/ci-integration.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci-integration.yml b/.github/workflows/ci-integration.yml index 773affd0..9a961fe8 100644 --- a/.github/workflows/ci-integration.yml +++ b/.github/workflows/ci-integration.yml @@ -29,6 +29,7 @@ jobs: python-version: - "3.10" - "3.11" + - "3.12" steps: - uses: actions/checkout@v2 From 5b5f27c7e0e8a350fa99c0cd4e98edf6a9ef107b Mon Sep 17 00:00:00 2001 From: David Dotson Date: Wed, 24 Jul 2024 16:11:06 -0700 Subject: [PATCH 04/18] Bump openmmforcefields to v0.14.1 in all conda envs --- devtools/conda-envs/alchemiscale-client.yml | 2 +- devtools/conda-envs/alchemiscale-compute.yml | 2 +- devtools/conda-envs/alchemiscale-server.yml | 2 +- devtools/conda-envs/test.yml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/devtools/conda-envs/alchemiscale-client.yml b/devtools/conda-envs/alchemiscale-client.yml index 2c2529c3..289ee084 100644 --- a/devtools/conda-envs/alchemiscale-client.yml +++ b/devtools/conda-envs/alchemiscale-client.yml @@ -10,7 +10,7 @@ dependencies: # alchemiscale dependencies - gufe=1.0.0 - openfe=1.0.1 - - openmmforcefields>=0.12.0 + - openmmforcefields>=0.14.1 - requests - click - httpx diff --git a/devtools/conda-envs/alchemiscale-compute.yml b/devtools/conda-envs/alchemiscale-compute.yml index 239c03d9..a1ee3303 100644 --- a/devtools/conda-envs/alchemiscale-compute.yml +++ b/devtools/conda-envs/alchemiscale-compute.yml @@ -10,7 +10,7 @@ dependencies: # alchemiscale dependencies - gufe=1.0.0 - openfe=1.0.1 - - openmmforcefields>=0.12.0 + - openmmforcefields>=0.14.1 - requests - click - httpx diff --git a/devtools/conda-envs/alchemiscale-server.yml b/devtools/conda-envs/alchemiscale-server.yml index b89db17b..838e335d 100644 --- a/devtools/conda-envs/alchemiscale-server.yml +++ b/devtools/conda-envs/alchemiscale-server.yml @@ -11,7 +11,7 @@ dependencies: - gufe=1.0.0 - openfe=1.0.1 - - openmmforcefields>=0.12.0 + - openmmforcefields>=0.14.1 - requests - click - pydantic<2.0 diff --git a/devtools/conda-envs/test.yml b/devtools/conda-envs/test.yml index fdab69d7..ad3d5182 100644 --- a/devtools/conda-envs/test.yml +++ b/devtools/conda-envs/test.yml @@ -9,7 +9,7 @@ dependencies: # alchemiscale dependencies - gufe>=1.0.0 - openfe>=1.0.1 - - openmmforcefields>=0.12.0 + - openmmforcefields>=0.14.1 - pydantic<2.0 ## state store From ce2e4584fceb71f540901f5724c7fe92d367771a Mon Sep 17 00:00:00 2001 From: David Dotson Date: Fri, 26 Jul 2024 17:47:53 -0700 Subject: [PATCH 05/18] Adding feflow main for now; will add release pin once we have one --- devtools/conda-envs/alchemiscale-client.yml | 1 + devtools/conda-envs/alchemiscale-compute.yml | 1 + devtools/conda-envs/alchemiscale-server.yml | 1 + devtools/conda-envs/test.yml | 1 + 4 files changed, 4 insertions(+) diff --git a/devtools/conda-envs/alchemiscale-client.yml b/devtools/conda-envs/alchemiscale-client.yml index 289ee084..86a57ddd 100644 --- a/devtools/conda-envs/alchemiscale-client.yml +++ b/devtools/conda-envs/alchemiscale-client.yml @@ -23,3 +23,4 @@ dependencies: - nest_asyncio - async_lru - git+https://github.com/openforcefield/alchemiscale.git@v0.5.0-beta.1 + - git+https://github.com/choderalab/feflow.git@main diff --git a/devtools/conda-envs/alchemiscale-compute.yml b/devtools/conda-envs/alchemiscale-compute.yml index a1ee3303..9fb02aaf 100644 --- a/devtools/conda-envs/alchemiscale-compute.yml +++ b/devtools/conda-envs/alchemiscale-compute.yml @@ -19,3 +19,4 @@ dependencies: - pip: - async_lru - git+https://github.com/openforcefield/alchemiscale.git@v0.5.0-beta.1 + - git+https://github.com/choderalab/feflow.git@main diff --git a/devtools/conda-envs/alchemiscale-server.yml b/devtools/conda-envs/alchemiscale-server.yml index 838e335d..8d989c6c 100644 --- a/devtools/conda-envs/alchemiscale-server.yml +++ b/devtools/conda-envs/alchemiscale-server.yml @@ -39,3 +39,4 @@ dependencies: - pip: - async_lru - git+https://github.com/openforcefield/alchemiscale.git@v0.5.0-beta.1 + - git+https://github.com/choderalab/feflow.git@main diff --git a/devtools/conda-envs/test.yml b/devtools/conda-envs/test.yml index ad3d5182..662f08d2 100644 --- a/devtools/conda-envs/test.yml +++ b/devtools/conda-envs/test.yml @@ -50,3 +50,4 @@ dependencies: - async_lru - git+https://github.com/datryllic/grolt@neo4j-5.x # neo4j test server deployment - git+https://github.com/OpenFreeEnergy/openfe-benchmarks + - git+https://github.com/choderalab/feflow.git@main From 4e60597c9a9f0ff10c5b2452488d684cf6f70fab Mon Sep 17 00:00:00 2001 From: David Dotson Date: Tue, 30 Jul 2024 22:43:36 -0700 Subject: [PATCH 06/18] Added alchemiscale-fah as a pip install Also pinned openmm to 8.1.2 --- devtools/conda-envs/alchemiscale-client.yml | 8 ++++++-- devtools/conda-envs/alchemiscale-compute.yml | 8 ++++++-- devtools/conda-envs/alchemiscale-server.yml | 8 ++++++-- devtools/conda-envs/test.yml | 6 +++++- 4 files changed, 23 insertions(+), 7 deletions(-) diff --git a/devtools/conda-envs/alchemiscale-client.yml b/devtools/conda-envs/alchemiscale-client.yml index 86a57ddd..25bae59d 100644 --- a/devtools/conda-envs/alchemiscale-client.yml +++ b/devtools/conda-envs/alchemiscale-client.yml @@ -10,7 +10,6 @@ dependencies: # alchemiscale dependencies - gufe=1.0.0 - openfe=1.0.1 - - openmmforcefields>=0.14.1 - requests - click - httpx @@ -19,8 +18,13 @@ dependencies: ## user client printing - rich + # additional pins + - openmm=8.1.2 + - openmmforcefields>=0.14.1 + - pip: - nest_asyncio - async_lru - - git+https://github.com/openforcefield/alchemiscale.git@v0.5.0-beta.1 + - git+https://github.com/openforcefield/alchemiscale.git@release-0.5.0-prep - git+https://github.com/choderalab/feflow.git@main + - git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a diff --git a/devtools/conda-envs/alchemiscale-compute.yml b/devtools/conda-envs/alchemiscale-compute.yml index 9fb02aaf..1eabc4da 100644 --- a/devtools/conda-envs/alchemiscale-compute.yml +++ b/devtools/conda-envs/alchemiscale-compute.yml @@ -10,13 +10,17 @@ dependencies: # alchemiscale dependencies - gufe=1.0.0 - openfe=1.0.1 - - openmmforcefields>=0.14.1 - requests - click - httpx - pydantic<2.0 + # additional pins + - openmm=8.1.2 + - openmmforcefields>=0.14.1 + - pip: - async_lru - - git+https://github.com/openforcefield/alchemiscale.git@v0.5.0-beta.1 + - git+https://github.com/openforcefield/alchemiscale.git@release-0.5.0-prep - git+https://github.com/choderalab/feflow.git@main + - git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a diff --git a/devtools/conda-envs/alchemiscale-server.yml b/devtools/conda-envs/alchemiscale-server.yml index 8d989c6c..5c3cc267 100644 --- a/devtools/conda-envs/alchemiscale-server.yml +++ b/devtools/conda-envs/alchemiscale-server.yml @@ -11,7 +11,6 @@ dependencies: - gufe=1.0.0 - openfe=1.0.1 - - openmmforcefields>=0.14.1 - requests - click - pydantic<2.0 @@ -36,7 +35,12 @@ dependencies: - httpx - cryptography + # additional pins + - openmm=8.1.2 + - openmmforcefields>=0.14.1 + - pip: - async_lru - - git+https://github.com/openforcefield/alchemiscale.git@v0.5.0-beta.1 + - git+https://github.com/openforcefield/alchemiscale.git@release-0.5.0-prep - git+https://github.com/choderalab/feflow.git@main + - git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a diff --git a/devtools/conda-envs/test.yml b/devtools/conda-envs/test.yml index 662f08d2..084aa9dc 100644 --- a/devtools/conda-envs/test.yml +++ b/devtools/conda-envs/test.yml @@ -9,7 +9,6 @@ dependencies: # alchemiscale dependencies - gufe>=1.0.0 - openfe>=1.0.1 - - openmmforcefields>=0.14.1 - pydantic<2.0 ## state store @@ -46,8 +45,13 @@ dependencies: - coverage - moto + # additional pins + - openmm=8.1.2 + - openmmforcefields>=0.14.1 + - pip: - async_lru - git+https://github.com/datryllic/grolt@neo4j-5.x # neo4j test server deployment - git+https://github.com/OpenFreeEnergy/openfe-benchmarks - git+https://github.com/choderalab/feflow.git@main + - git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a From 6d3db0f732f459f31e13f398ce0d984b61ac6234 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Wed, 31 Jul 2024 15:00:50 -0700 Subject: [PATCH 07/18] Make sure we grab the right feflow version --- devtools/conda-envs/alchemiscale-client.yml | 2 +- devtools/conda-envs/alchemiscale-compute.yml | 2 +- devtools/conda-envs/alchemiscale-server.yml | 2 +- devtools/conda-envs/test.yml | 4 ++-- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/devtools/conda-envs/alchemiscale-client.yml b/devtools/conda-envs/alchemiscale-client.yml index 25bae59d..c938a662 100644 --- a/devtools/conda-envs/alchemiscale-client.yml +++ b/devtools/conda-envs/alchemiscale-client.yml @@ -26,5 +26,5 @@ dependencies: - nest_asyncio - async_lru - git+https://github.com/openforcefield/alchemiscale.git@release-0.5.0-prep - - git+https://github.com/choderalab/feflow.git@main + - git+https://github.com/choderalab/feflow.git@0.1.0 - git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a diff --git a/devtools/conda-envs/alchemiscale-compute.yml b/devtools/conda-envs/alchemiscale-compute.yml index 1eabc4da..eb780d74 100644 --- a/devtools/conda-envs/alchemiscale-compute.yml +++ b/devtools/conda-envs/alchemiscale-compute.yml @@ -22,5 +22,5 @@ dependencies: - pip: - async_lru - git+https://github.com/openforcefield/alchemiscale.git@release-0.5.0-prep - - git+https://github.com/choderalab/feflow.git@main + - git+https://github.com/choderalab/feflow.git@0.1.0 - git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a diff --git a/devtools/conda-envs/alchemiscale-server.yml b/devtools/conda-envs/alchemiscale-server.yml index 5c3cc267..39e090d9 100644 --- a/devtools/conda-envs/alchemiscale-server.yml +++ b/devtools/conda-envs/alchemiscale-server.yml @@ -42,5 +42,5 @@ dependencies: - pip: - async_lru - git+https://github.com/openforcefield/alchemiscale.git@release-0.5.0-prep - - git+https://github.com/choderalab/feflow.git@main + - git+https://github.com/choderalab/feflow.git@0.1.0 - git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a diff --git a/devtools/conda-envs/test.yml b/devtools/conda-envs/test.yml index 084aa9dc..1603e735 100644 --- a/devtools/conda-envs/test.yml +++ b/devtools/conda-envs/test.yml @@ -53,5 +53,5 @@ dependencies: - async_lru - git+https://github.com/datryllic/grolt@neo4j-5.x # neo4j test server deployment - git+https://github.com/OpenFreeEnergy/openfe-benchmarks - - git+https://github.com/choderalab/feflow.git@main - - git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a + - git+https://github.com/choderalab/feflow.git + - git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a # temporary From 2c458d1473fde8fb3359f603fca44d37fa2c6cd3 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Thu, 1 Aug 2024 11:19:47 -0700 Subject: [PATCH 08/18] Troubleshooting issues with API services Attempting to pin gunicorn and uvicorn to previously-known working versions. --- devtools/conda-envs/alchemiscale-server.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/devtools/conda-envs/alchemiscale-server.yml b/devtools/conda-envs/alchemiscale-server.yml index 39e090d9..bccc8146 100644 --- a/devtools/conda-envs/alchemiscale-server.yml +++ b/devtools/conda-envs/alchemiscale-server.yml @@ -25,8 +25,8 @@ dependencies: ## api(s) - fastapi - - uvicorn - - gunicorn + - uvicorn=0.29.0 + - gunicorn=21.2.0 - python-jose - passlib - bcrypt From c8366449d644453122d0209a879c3a3f401934b8 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Thu, 1 Aug 2024 11:50:40 -0700 Subject: [PATCH 09/18] Switching to python 3.10; still seeing issues with API services --- 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 c938a662..7631d81b 100644 --- a/devtools/conda-envs/alchemiscale-client.yml +++ b/devtools/conda-envs/alchemiscale-client.yml @@ -5,7 +5,7 @@ channels: dependencies: - pip - - python =3.11 + - python =3.10 # alchemiscale dependencies - gufe=1.0.0 diff --git a/devtools/conda-envs/alchemiscale-compute.yml b/devtools/conda-envs/alchemiscale-compute.yml index eb780d74..aaaa3374 100644 --- a/devtools/conda-envs/alchemiscale-compute.yml +++ b/devtools/conda-envs/alchemiscale-compute.yml @@ -4,7 +4,7 @@ channels: dependencies: - pip - - python =3.11 + - python =3.10 - cudatoolkit =11.8 # alchemiscale dependencies diff --git a/devtools/conda-envs/alchemiscale-server.yml b/devtools/conda-envs/alchemiscale-server.yml index bccc8146..be3b941b 100644 --- a/devtools/conda-envs/alchemiscale-server.yml +++ b/devtools/conda-envs/alchemiscale-server.yml @@ -5,7 +5,7 @@ channels: dependencies: - pip - - python =3.11 + - python =3.10 # alchemiscale dependencies - gufe=1.0.0 From 7652a4c51584d6cbcfa7ee75d8cbac026193951b Mon Sep 17 00:00:00 2001 From: David Dotson Date: Mon, 5 Aug 2024 16:17:41 -0700 Subject: [PATCH 10/18] Added curl explicitly to environment for alchemiscale-server --- devtools/conda-envs/alchemiscale-server.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/devtools/conda-envs/alchemiscale-server.yml b/devtools/conda-envs/alchemiscale-server.yml index be3b941b..25ad8801 100644 --- a/devtools/conda-envs/alchemiscale-server.yml +++ b/devtools/conda-envs/alchemiscale-server.yml @@ -39,6 +39,9 @@ dependencies: - openmm=8.1.2 - openmmforcefields>=0.14.1 + # deployment + - curl # used in healthchecks for API services + - pip: - async_lru - git+https://github.com/openforcefield/alchemiscale.git@release-0.5.0-prep From 2d09447b41dee202ec87a332ba9c4e68b8473638 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Mon, 5 Aug 2024 18:39:37 -0700 Subject: [PATCH 11/18] Added alchemiscale-fah deps to client and server envs --- devtools/conda-envs/alchemiscale-client.yml | 4 ++++ devtools/conda-envs/alchemiscale-server.yml | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/devtools/conda-envs/alchemiscale-client.yml b/devtools/conda-envs/alchemiscale-client.yml index 7631d81b..de6509fd 100644 --- a/devtools/conda-envs/alchemiscale-client.yml +++ b/devtools/conda-envs/alchemiscale-client.yml @@ -22,6 +22,10 @@ dependencies: - openmm=8.1.2 - openmmforcefields>=0.14.1 + # alchemiscale-fah dependencies + - cryptography + - plyvel + - pip: - nest_asyncio - async_lru diff --git a/devtools/conda-envs/alchemiscale-server.yml b/devtools/conda-envs/alchemiscale-server.yml index 25ad8801..99bd33af 100644 --- a/devtools/conda-envs/alchemiscale-server.yml +++ b/devtools/conda-envs/alchemiscale-server.yml @@ -42,6 +42,10 @@ dependencies: # deployment - curl # used in healthchecks for API services + # alchemiscale-fah dependencies + - cryptography + - plyvel + - pip: - async_lru - git+https://github.com/openforcefield/alchemiscale.git@release-0.5.0-prep From dca3f347cceeac8f73921771d28d61238dd5fdea Mon Sep 17 00:00:00 2001 From: David Dotson Date: Fri, 9 Aug 2024 14:34:49 -0700 Subject: [PATCH 12/18] Updates to prod env pins in anticipation of release --- devtools/conda-envs/alchemiscale-client.yml | 8 +++++--- devtools/conda-envs/alchemiscale-compute.yml | 7 +++++-- devtools/conda-envs/alchemiscale-server.yml | 11 +++++++---- devtools/conda-envs/test.yml | 6 ++++-- 4 files changed, 21 insertions(+), 11 deletions(-) diff --git a/devtools/conda-envs/alchemiscale-client.yml b/devtools/conda-envs/alchemiscale-client.yml index de6509fd..d43c222f 100644 --- a/devtools/conda-envs/alchemiscale-client.yml +++ b/devtools/conda-envs/alchemiscale-client.yml @@ -5,7 +5,7 @@ channels: dependencies: - pip - - python =3.10 + - python=3.12 # alchemiscale dependencies - gufe=1.0.0 @@ -15,6 +15,9 @@ dependencies: - httpx - pydantic<2.0 + # openmm protocols + - feflow=0.1.0 + ## user client printing - rich @@ -30,5 +33,4 @@ dependencies: - nest_asyncio - async_lru - git+https://github.com/openforcefield/alchemiscale.git@release-0.5.0-prep - - git+https://github.com/choderalab/feflow.git@0.1.0 - - git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a + #- git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a diff --git a/devtools/conda-envs/alchemiscale-compute.yml b/devtools/conda-envs/alchemiscale-compute.yml index aaaa3374..9e859b90 100644 --- a/devtools/conda-envs/alchemiscale-compute.yml +++ b/devtools/conda-envs/alchemiscale-compute.yml @@ -4,7 +4,7 @@ channels: dependencies: - pip - - python =3.10 + - python =3.12 - cudatoolkit =11.8 # alchemiscale dependencies @@ -15,6 +15,9 @@ dependencies: - httpx - pydantic<2.0 + # openmm protocols + - feflow=0.1.0 + # additional pins - openmm=8.1.2 - openmmforcefields>=0.14.1 @@ -23,4 +26,4 @@ dependencies: - async_lru - git+https://github.com/openforcefield/alchemiscale.git@release-0.5.0-prep - git+https://github.com/choderalab/feflow.git@0.1.0 - - git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a + #- git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a diff --git a/devtools/conda-envs/alchemiscale-server.yml b/devtools/conda-envs/alchemiscale-server.yml index 99bd33af..b1bb18c1 100644 --- a/devtools/conda-envs/alchemiscale-server.yml +++ b/devtools/conda-envs/alchemiscale-server.yml @@ -5,7 +5,7 @@ channels: dependencies: - pip - - python =3.10 + - python=3.12 # alchemiscale dependencies - gufe=1.0.0 @@ -25,8 +25,8 @@ dependencies: ## api(s) - fastapi - - uvicorn=0.29.0 - - gunicorn=21.2.0 + - uvicorn + - gunicorn - python-jose - passlib - bcrypt @@ -35,6 +35,9 @@ dependencies: - httpx - cryptography + # openmm protocols + - feflow=0.1.0 + # additional pins - openmm=8.1.2 - openmmforcefields>=0.14.1 @@ -50,4 +53,4 @@ dependencies: - async_lru - git+https://github.com/openforcefield/alchemiscale.git@release-0.5.0-prep - git+https://github.com/choderalab/feflow.git@0.1.0 - - git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a + #- git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a diff --git a/devtools/conda-envs/test.yml b/devtools/conda-envs/test.yml index 1603e735..7a8a6d6a 100644 --- a/devtools/conda-envs/test.yml +++ b/devtools/conda-envs/test.yml @@ -35,6 +35,9 @@ dependencies: - httpx - cryptography + # openmm protocols + - feflow>=0.1.0 + ## cli - click @@ -53,5 +56,4 @@ dependencies: - async_lru - git+https://github.com/datryllic/grolt@neo4j-5.x # neo4j test server deployment - git+https://github.com/OpenFreeEnergy/openfe-benchmarks - - git+https://github.com/choderalab/feflow.git - - git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a # temporary + #- git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a # temporary From 842a9ccf21e2b32dd596c6eebc0defc919ddfe50 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Sun, 11 Aug 2024 14:44:07 -0700 Subject: [PATCH 13/18] Remove pip install of feflow from prod envs --- devtools/conda-envs/alchemiscale-compute.yml | 1 - devtools/conda-envs/alchemiscale-server.yml | 1 - 2 files changed, 2 deletions(-) diff --git a/devtools/conda-envs/alchemiscale-compute.yml b/devtools/conda-envs/alchemiscale-compute.yml index 9e859b90..1bd42e1b 100644 --- a/devtools/conda-envs/alchemiscale-compute.yml +++ b/devtools/conda-envs/alchemiscale-compute.yml @@ -25,5 +25,4 @@ dependencies: - pip: - async_lru - git+https://github.com/openforcefield/alchemiscale.git@release-0.5.0-prep - - git+https://github.com/choderalab/feflow.git@0.1.0 #- git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a diff --git a/devtools/conda-envs/alchemiscale-server.yml b/devtools/conda-envs/alchemiscale-server.yml index b1bb18c1..5f86bbd0 100644 --- a/devtools/conda-envs/alchemiscale-server.yml +++ b/devtools/conda-envs/alchemiscale-server.yml @@ -52,5 +52,4 @@ dependencies: - pip: - async_lru - git+https://github.com/openforcefield/alchemiscale.git@release-0.5.0-prep - - git+https://github.com/choderalab/feflow.git@0.1.0 #- git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a From dc43ef8d77e067e6313401439c7b1f2ed77ab6b1 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Mon, 12 Aug 2024 12:09:54 -0700 Subject: [PATCH 14/18] Re-add alchemiscale-fah to prod envs for now --- devtools/conda-envs/alchemiscale-client.yml | 2 +- devtools/conda-envs/alchemiscale-compute.yml | 2 +- devtools/conda-envs/alchemiscale-server.yml | 2 +- devtools/conda-envs/test.yml | 1 - 4 files changed, 3 insertions(+), 4 deletions(-) diff --git a/devtools/conda-envs/alchemiscale-client.yml b/devtools/conda-envs/alchemiscale-client.yml index d43c222f..1c989b83 100644 --- a/devtools/conda-envs/alchemiscale-client.yml +++ b/devtools/conda-envs/alchemiscale-client.yml @@ -33,4 +33,4 @@ dependencies: - nest_asyncio - async_lru - git+https://github.com/openforcefield/alchemiscale.git@release-0.5.0-prep - #- git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a + - git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a diff --git a/devtools/conda-envs/alchemiscale-compute.yml b/devtools/conda-envs/alchemiscale-compute.yml index 1bd42e1b..e00be1de 100644 --- a/devtools/conda-envs/alchemiscale-compute.yml +++ b/devtools/conda-envs/alchemiscale-compute.yml @@ -25,4 +25,4 @@ dependencies: - pip: - async_lru - git+https://github.com/openforcefield/alchemiscale.git@release-0.5.0-prep - #- git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a + - git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a diff --git a/devtools/conda-envs/alchemiscale-server.yml b/devtools/conda-envs/alchemiscale-server.yml index 5f86bbd0..b6ecdc63 100644 --- a/devtools/conda-envs/alchemiscale-server.yml +++ b/devtools/conda-envs/alchemiscale-server.yml @@ -52,4 +52,4 @@ dependencies: - pip: - async_lru - git+https://github.com/openforcefield/alchemiscale.git@release-0.5.0-prep - #- git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a + - git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a diff --git a/devtools/conda-envs/test.yml b/devtools/conda-envs/test.yml index 7a8a6d6a..a23320c2 100644 --- a/devtools/conda-envs/test.yml +++ b/devtools/conda-envs/test.yml @@ -56,4 +56,3 @@ dependencies: - async_lru - git+https://github.com/datryllic/grolt@neo4j-5.x # neo4j test server deployment - git+https://github.com/OpenFreeEnergy/openfe-benchmarks - #- git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a # temporary From 20f9d2169d3a23a932215336b2a8ee26e7c66160 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Mon, 12 Aug 2024 14:49:43 -0700 Subject: [PATCH 15/18] Set prod envs to use alchemiscale tag v0.5.0 --- devtools/conda-envs/alchemiscale-client.yml | 3 +-- devtools/conda-envs/alchemiscale-compute.yml | 3 +-- devtools/conda-envs/alchemiscale-server.yml | 3 +-- 3 files changed, 3 insertions(+), 6 deletions(-) diff --git a/devtools/conda-envs/alchemiscale-client.yml b/devtools/conda-envs/alchemiscale-client.yml index 1c989b83..a027bde5 100644 --- a/devtools/conda-envs/alchemiscale-client.yml +++ b/devtools/conda-envs/alchemiscale-client.yml @@ -32,5 +32,4 @@ dependencies: - pip: - nest_asyncio - async_lru - - git+https://github.com/openforcefield/alchemiscale.git@release-0.5.0-prep - - git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a + - git+https://github.com/openforcefield/alchemiscale.git@v0.5.0 diff --git a/devtools/conda-envs/alchemiscale-compute.yml b/devtools/conda-envs/alchemiscale-compute.yml index e00be1de..a44788d4 100644 --- a/devtools/conda-envs/alchemiscale-compute.yml +++ b/devtools/conda-envs/alchemiscale-compute.yml @@ -24,5 +24,4 @@ dependencies: - pip: - async_lru - - git+https://github.com/openforcefield/alchemiscale.git@release-0.5.0-prep - - git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a + - git+https://github.com/openforcefield/alchemiscale.git@v0.5.0 diff --git a/devtools/conda-envs/alchemiscale-server.yml b/devtools/conda-envs/alchemiscale-server.yml index b6ecdc63..7d46147c 100644 --- a/devtools/conda-envs/alchemiscale-server.yml +++ b/devtools/conda-envs/alchemiscale-server.yml @@ -51,5 +51,4 @@ dependencies: - pip: - async_lru - - git+https://github.com/openforcefield/alchemiscale.git@release-0.5.0-prep - - git+https://github.com/openforcefield/alchemiscale-fah.git@live-testing-alchemiscale-0.5.0-beta.a + - git+https://github.com/openforcefield/alchemiscale.git@v0.5.0 From 236b0eff7f92b659ff0135f1c4cc2f8ac167c459 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Mon, 12 Aug 2024 14:55:35 -0700 Subject: [PATCH 16/18] Remove deployment of conda envs, since Anaconda deprecated this feature Updated docs to reflect this. --- .github/workflows/deploy-conda-envs.yml | 75 ------------------------- docs/user_guide.rst | 18 +++--- 2 files changed, 7 insertions(+), 86 deletions(-) delete mode 100644 .github/workflows/deploy-conda-envs.yml diff --git a/.github/workflows/deploy-conda-envs.yml b/.github/workflows/deploy-conda-envs.yml deleted file mode 100644 index 15964545..00000000 --- a/.github/workflows/deploy-conda-envs.yml +++ /dev/null @@ -1,75 +0,0 @@ ---- - -name: Deployment - conda environments - -on: - push: - branches: - - master - paths: - - 'devtools/conda-envs/alchemiscale-*.yml' - workflow_dispatch: - -jobs: - deploy-conda-env: - runs-on: ubuntu-latest - strategy: - fail-fast: false - matrix: - env-name: - - alchemiscale-client - - alchemiscale-server - - alchemiscale-compute - steps: - - name: Checkout code - uses: actions/checkout@v2 - - - name: ensure we only have one instance running - uses: softprops/turnstyle@v1 - env: - GITHUB_TOKEN: ${{ secrets.GH_DANGERBOT_TOKEN_LIMITED }} - with: - abort-after-seconds: 60 - - #- name: Cache conda - # uses: actions/cache@v2 - # env: - # CACHE_NUMBER: 0 - # with: - # path: ~/conda_pkgs_dir - # key: - # ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ - # hashFiles('devtools/conda-envs/${{ matrix.env-name }}.yml') }} - - - name: Additional info about the build - shell: bash - run: | - uname -a - df -h - ulimit -a - - - name: Configure conda; test creation of environment - uses: conda-incubator/setup-miniconda@v2 - with: - #python-version: 3.9 - auto-update-conda: true - use-mamba: true - miniforge-variant: Mambaforge - activate-environment: ${{ matrix.env-name }} - environment-file: devtools/conda-envs/${{ matrix.env-name }}.yml - #use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly! - #auto-activate-base: false - - - name: Environment Information - shell: bash -l {0} - run: | - conda info - conda list - - - name: Deploy conda env - shell: bash -l {0} - env: - ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} - run: | - mamba install -y anaconda-client - anaconda -t ${ANACONDA_TOKEN} upload --user openforcefield devtools/conda-envs/${{ matrix.env-name }}.yml diff --git a/docs/user_guide.rst b/docs/user_guide.rst index 9a098e08..10355eea 100644 --- a/docs/user_guide.rst +++ b/docs/user_guide.rst @@ -12,27 +12,23 @@ It assumes that you already have a user identity on the target ``alchemiscale`` Installation ************ -Create a conda environment on your workstation:: - - $ conda env create openforcefield/alchemiscale-client - -You can also use ``mamba`` instead of conda above if you prefer a faster solver and have it installed, e.g. via `mambaforge`_. - -If this doesn’t work, clone alchemiscale from Github, and install from there:: +Clone alchemiscale from Github, and switch to the latest release tag:: $ git clone https://github.com/openforcefield/alchemiscale.git $ cd alchemiscale - $ git checkout v0.4.0 + $ git checkout v0.5.0 - $ conda env create -f devtools/conda-envs/alchemiscale-client.yml +Create a conda environment using, e.g. `micromamba`_:: + + $ micromamba create -f devtools/conda-envs/alchemiscale-client.yml Once installed, activate the environment:: - $ conda activate alchemiscale-client + $ micromamba activate alchemiscale-client You may wish to install other packages into this environment, such as jupyterlab. -.. _mambaforge: https://github.com/conda-forge/miniforge#mambaforge +.. _micromamba: https://github.com/mamba-org/micromamba-releases Installing on ARM-based Macs From 8f7ad24adf67c5c2724fc7a4ecfd8ab5094669e3 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Mon, 12 Aug 2024 15:05:03 -0700 Subject: [PATCH 17/18] Reverting to Python 3.11 just to be cautious. --- 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 a027bde5..a5c97780 100644 --- a/devtools/conda-envs/alchemiscale-client.yml +++ b/devtools/conda-envs/alchemiscale-client.yml @@ -5,7 +5,7 @@ channels: dependencies: - pip - - python=3.12 + - python=3.11 # alchemiscale dependencies - gufe=1.0.0 diff --git a/devtools/conda-envs/alchemiscale-compute.yml b/devtools/conda-envs/alchemiscale-compute.yml index a44788d4..95a21c76 100644 --- a/devtools/conda-envs/alchemiscale-compute.yml +++ b/devtools/conda-envs/alchemiscale-compute.yml @@ -4,7 +4,7 @@ channels: dependencies: - pip - - python =3.12 + - python =3.11 - cudatoolkit =11.8 # alchemiscale dependencies diff --git a/devtools/conda-envs/alchemiscale-server.yml b/devtools/conda-envs/alchemiscale-server.yml index 7d46147c..e85dbf4a 100644 --- a/devtools/conda-envs/alchemiscale-server.yml +++ b/devtools/conda-envs/alchemiscale-server.yml @@ -5,7 +5,7 @@ channels: dependencies: - pip - - python=3.12 + - python=3.11 # alchemiscale dependencies - gufe=1.0.0 From 01373df2cce43dbdfb6b8b3f485720a59605b72b Mon Sep 17 00:00:00 2001 From: David Dotson Date: Mon, 12 Aug 2024 15:10:33 -0700 Subject: [PATCH 18/18] Switch prod envs back to Python 3.12 --- 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 a5c97780..a027bde5 100644 --- a/devtools/conda-envs/alchemiscale-client.yml +++ b/devtools/conda-envs/alchemiscale-client.yml @@ -5,7 +5,7 @@ channels: dependencies: - pip - - python=3.11 + - python=3.12 # alchemiscale dependencies - gufe=1.0.0 diff --git a/devtools/conda-envs/alchemiscale-compute.yml b/devtools/conda-envs/alchemiscale-compute.yml index 95a21c76..a44788d4 100644 --- a/devtools/conda-envs/alchemiscale-compute.yml +++ b/devtools/conda-envs/alchemiscale-compute.yml @@ -4,7 +4,7 @@ channels: dependencies: - pip - - python =3.11 + - python =3.12 - cudatoolkit =11.8 # alchemiscale dependencies diff --git a/devtools/conda-envs/alchemiscale-server.yml b/devtools/conda-envs/alchemiscale-server.yml index e85dbf4a..7d46147c 100644 --- a/devtools/conda-envs/alchemiscale-server.yml +++ b/devtools/conda-envs/alchemiscale-server.yml @@ -5,7 +5,7 @@ channels: dependencies: - pip - - python=3.11 + - python=3.12 # alchemiscale dependencies - gufe=1.0.0