Merge branch 'master' into margo/readjson

hcs-t4sg · Oct 8, 2023 · 4ee6c29 · 4ee6c29
2 parents b243bb3 + 54049f2
commit 4ee6c29
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Showing 23 changed files with 104 additions and 57 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -25,7 +25,8 @@ jobs:
           name: Install ersilia package in developer mode
           command: |
               source activate ersilia
-              pip install -e .
+              pip install -U pip setuptools
+              python -m pip install -e .
       - run:
           name: Test CLI
           command: |
@@ -63,12 +64,6 @@ jobs:
           command: |
               source activate ersilia
               ersilia -v delete molecular-weight
-      - run:
-          name: Test Python interface
-          command: |
-            source activate ersilia
-            pip install -e .[test]
-            pytest
   docs-build:
     docker:
       - image: ersiliaos/conda:3.7
@@ -79,6 +74,7 @@ jobs:
           command: |
               apt-get update
               source activate ersilia
+              pip install -U pip setuptools
               pip install -e .[docs]
               apt-get -y install make
       - run:

diff --git a/.github/workflows/approve-dispatch.yml b/.github/workflows/approve-dispatch.yml
@@ -13,11 +13,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@3df4ab11eba7bda6032a0b82a6bb43b11571feac # [email protected]
+        uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # [email protected]
 
       # parse the issue body from free form text to a structured JSON object
       - name: parse issue
-        uses: GrantBirki/[email protected].0
+        uses: GrantBirki/[email protected].1
         id: issue-parser
         with:
           body: ${{ github.event.client_payload.github.payload.issue.body }}
@@ -81,7 +81,7 @@ jobs:
 
       # upload git-lfs object
       - name: checkout persist credentials
-        uses: actions/checkout@3df4ab11eba7bda6032a0b82a6bb43b11571feac # [email protected]
+        uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # [email protected]
         with:
           persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
           fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
@@ -154,7 +154,7 @@ jobs:
 
       # comment on the issue comment with further instructions for the user
       - name: comment
-        uses: GrantBirki/comment@eab1bc94aa728cf526dcd6639bfd067512d4a5cb # [email protected].6
+        uses: GrantBirki/comment@e6bf4bc177996c9572b4ddb98b25eb1a80f9abc9 # [email protected].7
         with:
           issue-number: ${{ github.event.client_payload.github.payload.issue.number }}
           file: .github/templates/new-model.md

diff --git a/.github/workflows/black-code-formatter.yml b/.github/workflows/black-code-formatter.yml
@@ -0,0 +1,34 @@
+name: Python Black Linter
+
+on:
+  push:
+  pull_request:
+  issue_comment:
+    types: [ created, edited ]
+
+jobs:
+  lint:
+    if: ${{ !contains(github.event_name, 'issue_comment') }} # Don't want to trigger on comments
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: psf/black@stable
+        with:
+          options: "--check"
+          src: "./ersilia"
+  comment-lint:
+    if: ${{ github.event.issue.pull_request && contains(github.event.comment.body, '✨') }}
+    runs-on: ubuntu-latest
+    permissions:
+      # Give the default GITHUB_TOKEN write permission to commit and push the
+      # added or changed files to the repository.
+      contents: write
+    steps:
+      - name: Checkout branch
+        uses: actions/checkout@v3
+      - name: Lint files
+        uses: psf/black@stable
+        with:
+          src: "./ersilia"
+      - name: Commit lint
+        uses: stefanzweifel/git-auto-commit-action@v5
diff --git a/.github/workflows/ersilia-base-image-to-dockerhub.yml b/.github/workflows/ersilia-base-image-to-dockerhub.yml
@@ -11,17 +11,17 @@ jobs:
     steps:
       # https://github.com/docker/setup-qemu-action
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
 
       # https://github.com/docker/setup-buildx-action
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
 
       # log in to dockerhub
       - name: Login to Docker Hub
         if: github.event_name != 'pull_request'
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_PASSWORD }}
@@ -43,7 +43,7 @@ jobs:
             
       - name: Docker meta
         id: docker_meta
-        uses: docker/metadata-action@v4
+        uses: docker/metadata-action@v5
         with:
           # list of Docker images to use as base name for tags
           images: |
@@ -59,7 +59,7 @@ jobs:
             type=sha
             
       - name: Build and push
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           context: .
           platforms: linux/amd64,linux/arm64

diff --git a/.github/workflows/ersilia-installer-to-dockerhub.yml b/.github/workflows/ersilia-installer-to-dockerhub.yml
@@ -13,17 +13,17 @@ jobs:
     steps:
       # https://github.com/docker/setup-qemu-action
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
 
       # https://github.com/docker/setup-buildx-action
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
 
       # log in to dockerhub
       - name: Login to Docker Hub
         if: github.event_name != 'pull_request'
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_PASSWORD }}
@@ -47,7 +47,7 @@ jobs:
             
       - name: Docker meta
         id: docker_meta
-        uses: docker/metadata-action@v4
+        uses: docker/metadata-action@v5
         with:
           # list of Docker images to use as base name for tags
           images: |
@@ -63,7 +63,7 @@ jobs:
             type=sha
             
       - name: Build and push
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           context: .
           platforms: linux/amd64,linux/arm64

diff --git a/.github/workflows/install.yml b/.github/workflows/install.yml
@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@3df4ab11eba7bda6032a0b82a6bb43b11571feac
+    - uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@61a6322f88396a6271a6ee3565807d608ecaddd1
       with:
@@ -35,7 +35,7 @@ jobs:
         python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@3df4ab11eba7bda6032a0b82a6bb43b11571feac
+    - uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@61a6322f88396a6271a6ee3565807d608ecaddd1
       with:
@@ -57,7 +57,7 @@ jobs:
         platform: [ubuntu-latest, macos-latest]
     runs-on: ${{ matrix.platform }}
     steps:
-      - uses: actions/checkout@3df4ab11eba7bda6032a0b82a6bb43b11571feac # [email protected]
+      - uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # [email protected]
 
       - name: Add conda to system path
         run: echo $CONDA/bin >> $GITHUB_PATH

diff --git a/.github/workflows/json-check.yml b/.github/workflows/json-check.yml
@@ -15,10 +15,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: checkout
-        uses: actions/checkout@3df4ab11eba7bda6032a0b82a6bb43b11571feac # [email protected]
+        uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # [email protected]
 
       - name: json syntax check
-        uses: GrantBirki/json-yaml-validate@1652fde01b1be71dfa7131148819e67639792673 # [email protected].0
+        uses: GrantBirki/json-yaml-validate@3add42f5fa8bfff04a3fe664d27a316736257ef1 # [email protected].1
         with:
           exclude_file: ".github/config/exclude.txt" # .gitignore style file for exclusions
           comment: "true" # allow PR comments with error messages
diff --git a/.github/workflows/pr_check.yml b/.github/workflows/pr_check.yml
@@ -15,7 +15,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@3df4ab11eba7bda6032a0b82a6bb43b11571feac # [email protected]
+      - uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # [email protected]
 
       - name: Add conda to system path
         run: echo $CONDA/bin >> $GITHUB_PATH

diff --git a/.github/workflows/predict-model-input.yml b/.github/workflows/predict-model-input.yml
@@ -18,7 +18,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@3df4ab11eba7bda6032a0b82a6bb43b11571feac # [email protected]
+      - uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # [email protected]
 
       - name: Add conda to system path
         run: echo $CONDA/bin >> $GITHUB_PATH
@@ -44,14 +44,16 @@ jobs:
           python --version
           echo "After conda init"
           conda init
-          python -m pip install -e .[test]
+          python -m pip install -e .
 
       - name: Predict output
         run: |
           source activate
           echo "Sample model id selected: $MODEL_ID"
-          ersilia fetch $MODEL_ID
+          ersilia -v fetch $MODEL_ID
+          echo "Serving model: $MODEL_ID"
           ersilia serve $MODEL_ID
+          echo "$MODEL_ID successfully fetched and served"
           ersilia sample -n 100 -f input.csv
-          ersilia api -i input.csv -o output.csv
+          ersilia run -i input.csv -o output.csv
           ersilia close
diff --git a/.github/workflows/predict-model.yml b/.github/workflows/predict-model.yml
@@ -16,7 +16,7 @@ jobs:
         count: [0, 1, 2, 3, 4]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@3df4ab11eba7bda6032a0b82a6bb43b11571feac # [email protected]
+      - uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # [email protected]
 
       - name: Add conda to system path
         run: echo $CONDA/bin >> $GITHUB_PATH

diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@3df4ab11eba7bda6032a0b82a6bb43b11571feac # [email protected]
+      - uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # [email protected]
 
       - name: Set up Python
         uses: actions/setup-python@61a6322f88396a6271a6ee3565807d608ecaddd1 # [email protected]

diff --git a/.github/workflows/quick-manual-model-test.yml b/.github/workflows/quick-manual-model-test.yml
@@ -18,7 +18,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@3df4ab11eba7bda6032a0b82a6bb43b11571feac # [email protected]
+      - uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # [email protected]
 
       - name: Add conda to system path
         run: echo $CONDA/bin >> $GITHUB_PATH
@@ -58,7 +58,7 @@ jobs:
 
       - name: Upload log output
         if: ${{ failure() }}
-        uses: actions/upload-artifact@0b7f8abb1508181956e8e162db84b466c27e18ce # [email protected].2
+        uses: actions/upload-artifact@a8a3f3ad30e3422c9c7b888a15615d19a852ae32 # [email protected].3
         with:
           name: ersilia-predict-logs
           path: /home/runner/eos/console.log
diff --git a/.github/workflows/tag-to-version.yml b/.github/workflows/tag-to-version.yml
@@ -13,7 +13,7 @@ jobs:
 
     steps:
       - name: Checkout persist credentials
-        uses: actions/checkout@3df4ab11eba7bda6032a0b82a6bb43b11571feac # [email protected]
+        uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # [email protected]
         with:
           persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
           fetch-depth: 0 # otherwise, you will failed to push refs to dest repo

diff --git a/.github/workflows/test-colab.yml b/.github/workflows/test-colab.yml
@@ -8,7 +8,7 @@ jobs:
   test-colab-notebook:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@3df4ab11eba7bda6032a0b82a6bb43b11571feac # [email protected]
+      - uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # [email protected]
       - name: Add conda to system path
         run: echo $CONDA/bin >> $GITHUB_PATH
 
@@ -33,14 +33,14 @@ jobs:
         run: jupyter nbconvert --to notebook --execute notebooks/test-colab-notebook-python-api.ipynb --output=output-python-api.ipynb --ExecutePreprocessor.timeout=-1
 
       - name: Upload Output of the Google Colab Notebook CLI
-        uses: actions/upload-artifact@0b7f8abb1508181956e8e162db84b466c27e18ce # [email protected].2
+        uses: actions/upload-artifact@a8a3f3ad30e3422c9c7b888a15615d19a852ae32 # [email protected].3
         with:
           name: output-cli.ipynb
           path: notebooks/output-cli.ipynb
           retention-days: 7
 
       - name: Upload Output of the Google Colab Notebook Python API
-        uses: actions/upload-artifact@0b7f8abb1508181956e8e162db84b466c27e18ce # [email protected].2
+        uses: actions/upload-artifact@a8a3f3ad30e3422c9c7b888a15615d19a852ae32 # [email protected].3
         with:
           name: output-python-api.ipynb
           path: notebooks/output-python-api.ipynb

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -11,7 +11,7 @@ jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@3df4ab11eba7bda6032a0b82a6bb43b11571feac # [email protected]
+      - uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # [email protected]
 
       - name: Add conda to system path
         run: echo $CONDA/bin >> $GITHUB_PATH

diff --git a/.github/workflows/write_secrets.yml b/.github/workflows/write_secrets.yml
@@ -21,7 +21,7 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@3df4ab11eba7bda6032a0b82a6bb43b11571feac # [email protected]
+      - uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # [email protected]
 
       # Write json file
       - name: Write secrets to json file

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 <div id="top"></div>
 <img src="https://raw.githubusercontent.com/ersilia-os/ersilia/master/assets/Ersilia_Plum.png" height="70">
 
-# Welcome to the Ersilia Model Hub
+# 🎉 Welcome to the Ersilia Model Hub! 🌟
 
 [![Donate](https://img.shields.io/badge/Donate-PayPal-green.svg)](https://www.paypal.com/uk/fundraiser/charity/4145012) [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg)](CODE_OF_CONDUCT.md) [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-yellow.svg)](https://www.gnu.org/licenses/agpl-3.0)
 [![PyPI version fury.io](https://badge.fury.io/py/ersilia.svg)](https://pypi.python.org/pypi/ersilia/) [![Python 3.7](https://img.shields.io/pypi/pyversions/ersilia
@@ -18,7 +18,10 @@
 
 ## Project Description
 
-The Ersilia Model Hub is a unified platform of pre-trained AI/ML models for infectious and neglected disease research. The end goal is to provide an open-source, low-code solution to access AI/ML models for **drug discovery**. The models embedded in the hub include both models published in the literature (with appropriate third party acknowledgement) and models developed by the Ersilia team or contributors.
+The [Ersilia Model Hub](https://ersilia.io) is a unified platform of pre-trained AI/ML models dedicated to 🦠 infectious and neglected disease research. Our mission is to offer an open-source, 🛠 low-code solution that provides seamless access to AI/ML models for 💊 drug discovery. Models housed in our hub come from two sources:
+
+1. 📚 Published models from literature (with due third-party acknowledgement)
+2. 🛠 Custom models developed by the **Ersilia team** or our valued contributors.
 
 * Read more about the project in the [Ersilia Book](https://ersilia.gitbook.io/ersilia-book/)
 * Browse available models in the [Ersilia Model Hub](https://ersilia.io/model-hub/)

diff --git a/ersilia/cli/commands/info.py b/ersilia/cli/commands/info.py
@@ -12,7 +12,9 @@ def info_cmd():
     @ersilia_cli.command(
         short_help="Get model information", help="Get model information"
     )
-    @click.option('--as_json', is_flag=True, default=False, help='Output as JSON format')
+    @click.option(
+        "--as_json", is_flag=True, default=False, help="Output as JSON format"
+    )
     def info(as_json):
         session = Session(config_json=None)
         model_id = session.current_model_id()
@@ -26,4 +28,4 @@ def info(as_json):
             print(json.dumps(info, indent=4))
             return info
         else:
-            InformationDisplayer(info).echo()
+            InformationDisplayer(info).echo()
diff --git a/ersilia/cli/commands/run.py b/ersilia/cli/commands/run.py
@@ -33,8 +33,15 @@ def run(input, output, batch_size, track_run):
                 fg="red",
             )
             return
-        mdl = ErsiliaModel(model_id, service_class=service_class, config_json=None, track_runs=track_run)
-        result = mdl.run(input=input, output=output, batch_size=batch_size, track_run=track_run)
+        mdl = ErsiliaModel(
+            model_id,
+            service_class=service_class,
+            config_json=None,
+            track_runs=track_run,
+        )
+        result = mdl.run(
+            input=input, output=output, batch_size=batch_size, track_run=track_run
+        )
         if isinstance(result, types.GeneratorType):
             for result in mdl.run(input=input, output=output, batch_size=batch_size):
                 if result is not None: