Merge pull request OpenFreeEnergy#308 from OpenFreeEnergy/deployment-…

…openfe-1.1.0 Deploy openfe 1.1.0, update deployment apparatus for OpenFreeEnergy namespace
hmacdope · Sep 27, 2024 · 19c1f22 · 19c1f22
2 parents 5701fca + 4384409
commit 19c1f22
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diff --git a/.github/workflows/ci-integration.yml b/.github/workflows/ci-integration.yml
@@ -53,7 +53,7 @@ jobs:
           pytest -v --cov=alchemiscale --cov-report=xml alchemiscale/tests
 
       - name: codecov
-        if: ${{ github.repository == 'openforcefield/alchemiscale'
+        if: ${{ github.repository == 'OpenFreeEnergy/alchemiscale'
                 && github.event != 'schedule' }}
         uses: codecov/codecov-action@v2
         with:

diff --git a/.github/workflows/deploy-docker.yml b/.github/workflows/deploy-docker.yml
@@ -16,7 +16,7 @@ on:
 
 env:
   REGISTRY: ghcr.io
-  NAMESPACE: openforcefield
+  NAMESPACE: OpenFreeEnergy
 
 jobs:
   build-and-push-image:
@@ -39,15 +39,15 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Log in to the Container registry
-        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        uses: docker/login-action@v3
         with:
           registry: ${{ env.REGISTRY }}
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        uses: docker/metadata-action@v5
         with:
           images: ${{ env.REGISTRY }}/${{ env.NAMESPACE }}/${{ matrix.image }}
           tags: |

diff --git a/README.md b/README.md
@@ -2,8 +2,8 @@
 
 ---
 
-[![build](https://github.com/openforcefield/alchemiscale/actions/workflows/ci-integration.yml/badge.svg)](https://github.com/openforcefield/alchemiscale/actions/workflows/ci-integration.yml)
-[![coverage](https://codecov.io/gh/openforcefield/alchemiscale/branch/main/graph/badge.svg)](https://codecov.io/gh/openforcefield/alchemiscale)
+[![build](https://github.com/OpenFreeEnergy/alchemiscale/actions/workflows/ci-integration.yml/badge.svg)](https://github.com/OpenFreeEnergy/alchemiscale/actions/workflows/ci-integration.yml)
+[![coverage](https://codecov.io/gh/OpenFreeEnergy/alchemiscale/branch/main/graph/badge.svg)](https://codecov.io/gh/OpenFreeEnergy/alchemiscale)
 [![Documentation Status](https://readthedocs.org/projects/alchemiscale/badge/?version=latest)](https://alchemiscale.readthedocs.io/en/latest/?badge=latest)
 
 

diff --git a/devtools/conda-envs/alchemiscale-client.yml b/devtools/conda-envs/alchemiscale-client.yml
@@ -9,7 +9,7 @@ dependencies:
 
   # alchemiscale dependencies
   - gufe=1.0.0
-  - openfe=1.0.1
+  - openfe=1.1.0
   - requests
   - click
   - httpx
@@ -32,4 +32,4 @@ dependencies:
   - plyvel
 
   - pip:
-    - git+https://github.com/openforcefield/[email protected]
+    - git+https://github.com/OpenFreeEnergy/[email protected]
diff --git a/devtools/conda-envs/alchemiscale-compute.yml b/devtools/conda-envs/alchemiscale-compute.yml
@@ -9,7 +9,7 @@ dependencies:
 
   # alchemiscale dependencies
   - gufe=1.0.0
-  - openfe=1.0.1
+  - openfe=1.1.0
   - requests
   - click
   - httpx
@@ -24,4 +24,4 @@ dependencies:
   - openmmforcefields>=0.14.1
 
   - pip:
-    - git+https://github.com/openforcefield/[email protected]
+    - git+https://github.com/OpenFreeEnergy/[email protected]
diff --git a/devtools/conda-envs/alchemiscale-server.yml b/devtools/conda-envs/alchemiscale-server.yml
@@ -9,7 +9,7 @@ dependencies:
 
   # alchemiscale dependencies
   - gufe=1.0.0
-  - openfe=1.0.1
+  - openfe=1.1.0
 
   - requests
   - click
@@ -50,4 +50,4 @@ dependencies:
   - plyvel
 
   - pip:
-    - git+https://github.com/openforcefield/[email protected]
+    - git+https://github.com/OpenFreeEnergy/[email protected]
diff --git a/devtools/conda-envs/test.yml b/devtools/conda-envs/test.yml
@@ -8,7 +8,7 @@ dependencies:
 
   # alchemiscale dependencies
   - gufe>=1.0.0
-  - openfe>=1.0.1
+  - openfe>=1.1.0
   - pydantic<2.0
 
   ## state store

diff --git a/docker/alchemiscale-compute/Dockerfile b/docker/alchemiscale-compute/Dockerfile
@@ -1,7 +1,7 @@
-FROM mambaorg/micromamba:1.4.1
+FROM mambaorg/micromamba:1.5.10
 
-LABEL org.opencontainers.image.source=https://github.com/openforcefield/alchemiscale
-LABEL org.opencontainers.image.description="deployable compute services for an alchemiscale server"
+LABEL org.opencontainers.image.source=https://github.com/OpenFreeEnergy/alchemiscale
+LABEL org.opencontainers.image.description="deployable compute services for alchemiscale"
 LABEL org.opencontainers.image.licenses=MIT
 
 # Don't buffer stdout & stderr streams, so if there is a crash no partial buffer output is lost

diff --git a/docker/alchemiscale-server/.env.testing b/docker/alchemiscale-server/.env.testing
@@ -24,4 +24,4 @@ [email protected]
 HOST_DOMAIN=localhost
 
 # alchemiscale
-ALCHEMISCALE_DOCKER_IMAGE=ghcr.io/openforcefield/alchemiscale:feat-add_docker_compose
+ALCHEMISCALE_DOCKER_IMAGE=ghcr.io/OpenFreeEnergy/alchemiscale:latest
diff --git a/docker/alchemiscale-server/Dockerfile b/docker/alchemiscale-server/Dockerfile
@@ -1,6 +1,6 @@
-FROM mambaorg/micromamba:1.4.1
+FROM mambaorg/micromamba:1.5.10
 
-LABEL org.opencontainers.image.source=https://github.com/openforcefield/alchemiscale
+LABEL org.opencontainers.image.source=https://github.com/OpenFreeEnergy/alchemiscale
 LABEL org.opencontainers.image.description="a high-throughput alchemical free energy execution system for use with HPC, cloud, bare metal, and Folding@Home"
 LABEL org.opencontainers.image.licenses=MIT
 

diff --git a/docs/compute.rst b/docs/compute.rst
@@ -14,7 +14,7 @@ This documentation will expand over time as these variants become available; for
 In all cases, you will need to define a configuration file for your compute services to consume on startup.
 A template for this file can be found here; replace ``$ALCHEMISCALE_VERSION`` with the version tag, e.g. ``v0.1.4``, you have deployed for your server::
 
-    https://raw.githubusercontent.com/openforcefield/alchemiscale/$ALCHEMISCALE_VERSION/devtools/configs/synchronous-compute-settings.yaml
+    https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/$ALCHEMISCALE_VERSION/devtools/configs/synchronous-compute-settings.yaml
 
 
 ***********
@@ -35,7 +35,7 @@ Deploying with conda/mamba
 To deploy via ``conda``/``mamba``, first create an environment (we recommend ``mamba`` for its performance)::
 
     mamba env create -n alchemiscale-compute-$ALCHEMISCALE_VERSION \
-                     -f https://raw.githubusercontent.com/openforcefield/alchemiscale/$ALCHEMISCALE_VERSION/devtools/conda-envs/alchemiscale-compute.yml
+                     -f https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/$ALCHEMISCALE_VERSION/devtools/conda-envs/alchemiscale-compute.yml
 
 Once created, activate the environment in your current shell::
 
@@ -55,7 +55,7 @@ Assuming your configuration file is in the current working directory, to deploy
 
     docker run --gpus all \
                --rm \
-               -v $(pwd):/mnt ghcr.io/openforcefield/alchemiscale-compute:$ALCHEMISCALE_VERSION \
+               -v $(pwd):/mnt ghcr.io/OpenFreeEnergy/alchemiscale-compute:$ALCHEMISCALE_VERSION \
                compute synchronous -c /mnt/synchronous-compute-settings.yaml
 
 
@@ -157,7 +157,7 @@ We define a k8s `Deployment`_ featuring a single container spec as the file ``co
         spec:
           containers:
           - name: alchemiscale-synchronous-container
-            image: ghcr.io/openforcefield/alchemiscale-compute:$ALCHEMISCALE_VERSION
+            image: ghcr.io/OpenFreeEnergy/alchemiscale-compute:$ALCHEMISCALE_VERSION
             args: ["compute", "synchronous", "-c", "/mnt/settings/synchronous-compute-settings.yaml"]
             resources:
               limits:

diff --git a/docs/deployment.rst b/docs/deployment.rst
@@ -36,7 +36,7 @@ First install the `docker engine <https://docs.docker.com/engine/install/#server
 
 Now clone the repository and then navigate to the ``alchemiscale/docker/alchemiscale-server`` folder::
     
-    $ git clone https://github.com/openforcefield/alchemiscale.git
+    $ git clone https://github.com/OpenFreeEnergy/alchemiscale.git
     $ cd alchemiscale/docker/alchemiscale-server
 
 .. note ::

diff --git a/docs/development.rst b/docs/development.rst
@@ -180,7 +180,7 @@ This is directly analogous to the way users interact with ``alchemiscale`` via t
 Like the ``AlchemiscaleClient``, the ``AlchemiscaleComputeClient`` automatically handles authentication and JWT refreshes, retries, etc.
 
 
-.. _this template configuration: https://github.com/openforcefield/alchemiscale/blob/main/devtools/configs/synchronous-compute-settings.yaml
+.. _this template configuration: https://github.com/OpenFreeEnergy/alchemiscale/blob/main/devtools/configs/synchronous-compute-settings.yaml
 
 
 .. _library-layout:
@@ -248,10 +248,10 @@ The issue also functions as a convenient *anchor point* for maintainers to triag
 
 If the feature is of broad interest, or of interest to the maintainers themselves, you may find you don't have to implement it at all!
 
-.. _developed openly on GitHub: https://github.com/openforcefield/alchemiscale
-.. _New Contributors: https://github.com/openforcefield/alchemiscale/discussions/categories/new-contributors
-.. _open an issue: https://github.com/openforcefield/alchemiscale/issues
-.. _upcoming milestone: https://github.com/openforcefield/alchemiscale/milestones
+.. _developed openly on GitHub: https://github.com/OpenFreeEnergy/alchemiscale
+.. _New Contributors: https://github.com/OpenFreeEnergy/alchemiscale/discussions/categories/new-contributors
+.. _open an issue: https://github.com/OpenFreeEnergy/alchemiscale/issues
+.. _upcoming milestone: https://github.com/OpenFreeEnergy/alchemiscale/milestones
 
 Setting up your development environment
 =======================================
@@ -263,7 +263,7 @@ To develop new features, fix bugs, and advance the ``alchemiscale`` codebase, yo
 
 1. Clone the repository to your local machine::
 
-    $ git clone [email protected]:openforcefield/alchemiscale.git
+    $ git clone [email protected]:OpenFreeEnergy/alchemiscale.git
     $ cd alchemiscale
 
 2. Create a conda environment for running the test suite, preferrably with `mamba`_, and activate it::
@@ -294,5 +294,5 @@ Please be patient, and understand that it may take some time (weeks, even months
 
 
 .. _mamba: https://github.com/conda-forge/miniforge#mambaforge
-.. _known issues with developing on Mac: https://github.com/openforcefield/alchemiscale/issues/92
+.. _known issues with developing on Mac: https://github.com/OpenFreeEnergy/alchemiscale/issues/92
 .. _GitHub CLI: https://cli.github.com/
diff --git a/docs/user_guide.rst b/docs/user_guide.rst
@@ -14,7 +14,7 @@ Installation
 
 Clone alchemiscale from Github, and switch to the latest release tag::
 
-    $ git clone https://github.com/openforcefield/alchemiscale.git
+    $ git clone https://github.com/OpenFreeEnergy/alchemiscale.git
     $ cd alchemiscale
     $ git checkout v0.5.0
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -24,7 +24,7 @@ requires-python = ">= 3.9"
 dynamic = ["version"]
 
 [project.urls]
-Homepage = "https://github.com/openforcefield/alchemiscale"
+Homepage = "https://github.com/OpenFreeEnergy/alchemiscale"
 
 [project.optional-dependencies]
 test = [