From 91f14d828d819fb184e2a7bf2c89d97456cc5f77 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Tue, 22 Oct 2024 19:19:23 +0200 Subject: [PATCH 1/5] Switch to matching against `SettingsBaseModel` instead of `Settings` in `gufe_to_subgraph` --- alchemiscale/storage/statestore.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/alchemiscale/storage/statestore.py b/alchemiscale/storage/statestore.py index 87c00097..4e6b9c3c 100644 --- a/alchemiscale/storage/statestore.py +++ b/alchemiscale/storage/statestore.py @@ -18,9 +18,9 @@ AlchemicalNetwork, Transformation, NonTransformation, - Settings, Protocol, ) +from gufe.settings import SettingsBaseModel from gufe.tokenization import GufeTokenizable, GufeKey, JSON_HANDLER from neo4j import Transaction, GraphDatabase, Driver @@ -342,7 +342,7 @@ def _gufe_to_subgraph( ): node[key] = json.dumps(value, cls=JSON_HANDLER.encoder) node["_json_props"].append(key) - elif isinstance(value, Settings): + elif isinstance(value, SettingsBaseModel): node[key] = json.dumps(value, cls=JSON_HANDLER.encoder, sort_keys=True) node["_json_props"].append(key) elif isinstance(value, GufeTokenizable): From cbef297cd68d7d8a140c9082f0f742873fc24d33 Mon Sep 17 00:00:00 2001 From: Ian Kenney Date: Fri, 25 Oct 2024 08:06:29 -0700 Subject: [PATCH 2/5] Bump checkout action version to v4 --- .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 a91229af..d559b1bd 100644 --- a/.github/workflows/ci-integration.yml +++ b/.github/workflows/ci-integration.yml @@ -32,7 +32,7 @@ jobs: - "3.12" steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - uses: mamba-org/setup-micromamba@v1 with: From bdf8b16787e547a1c8fb94342fefd1985694c0d1 Mon Sep 17 00:00:00 2001 From: Ian Kenney Date: Fri, 25 Oct 2024 08:18:37 -0700 Subject: [PATCH 3/5] Pinning python-multipart to v0.0.12 CI is attempting to install 0.0.14 but versions 0.0.13 and 0.0.14 have been yanked from PyPI. --- 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 ec9a6955..7d117978 100644 --- a/devtools/conda-envs/test.yml +++ b/devtools/conda-envs/test.yml @@ -30,7 +30,7 @@ dependencies: - python-jose - passlib - bcrypt - - python-multipart + - python-multipart=0.0.12 - starlette - httpx - cryptography From 2d34bdd8a225a10cecd05652618f26a4eba7fd3c Mon Sep 17 00:00:00 2001 From: David Dotson Date: Fri, 25 Oct 2024 14:23:59 -0700 Subject: [PATCH 4/5] Add rationale for pinning python-multipart --- 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 7d117978..038d6acc 100644 --- a/devtools/conda-envs/test.yml +++ b/devtools/conda-envs/test.yml @@ -30,7 +30,7 @@ dependencies: - python-jose - passlib - bcrypt - - python-multipart=0.0.12 + - python-multipart=0.0.12 # temporarily pinned due to broken 0.14 release on conda-forge - starlette - httpx - cryptography From 8a5a28be7419985eada7672d5118160363c8cf62 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Fri, 25 Oct 2024 14:25:01 -0700 Subject: [PATCH 5/5] Pin python-multipart in server environment --- devtools/conda-envs/alchemiscale-server.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/devtools/conda-envs/alchemiscale-server.yml b/devtools/conda-envs/alchemiscale-server.yml index e7205497..2a68451b 100644 --- a/devtools/conda-envs/alchemiscale-server.yml +++ b/devtools/conda-envs/alchemiscale-server.yml @@ -31,7 +31,7 @@ dependencies: - python-jose - passlib - bcrypt - - python-multipart + - python-multipart=0.0.12 # temporarily pinned due to broken 0.14 release on conda-forge - starlette - httpx - cryptography