From c297a11bda6cee8d26bf99b5da45dc0dd2e7772a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 27 Sep 2023 10:14:13 +0000 Subject: [PATCH 01/24] Update levenshtein requirement from ^0.21.1 to >=0.21.1,<0.23.0 Updates the requirements on [levenshtein](https://github.com/maxbachmann/Levenshtein) to permit the latest version. - [Release notes](https://github.com/maxbachmann/Levenshtein/releases) - [Changelog](https://github.com/maxbachmann/Levenshtein/blob/main/HISTORY.md) - [Commits](https://github.com/maxbachmann/Levenshtein/compare/v0.21.1...v0.22.0) --- updated-dependencies: - dependency-name: levenshtein dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index cf1543ab9..9eb07620b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -47,7 +47,7 @@ pytest = {version = "^7.4.0", optional = true} fuzzywuzzy = {version = "^0.18.0", optional = true} sphinx = {version = ">=5.3.0", optional = true} # For compatibility with python 3.7.x jinja2 = {version = "^3.1.2", optional = true} -levenshtein = {version = "^0.21.1", optional = true} # For faster fuzzy search +levenshtein = {version = ">=0.21.1,<0.23.0", optional = true} # For faster fuzzy search boto3 = "^1.28.40" From 1503bb849d4abe2620fe3dccaded10147a5cd12f Mon Sep 17 00:00:00 2001 From: Raul Date: Thu, 28 Sep 2023 10:28:45 +1000 Subject: [PATCH 02/24] Updated predict-model-input.yml --- .github/workflows/predict-model-input.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/predict-model-input.yml b/.github/workflows/predict-model-input.yml index aceea9d71..79c9e4425 100644 --- a/.github/workflows/predict-model-input.yml +++ b/.github/workflows/predict-model-input.yml @@ -52,6 +52,7 @@ jobs: echo "Sample model id selected: $MODEL_ID" ersilia fetch $MODEL_ID ersilia serve $MODEL_ID + echo "$MODEL_ID succesfully fetched and served" ersilia sample -n 100 -f input.csv ersilia api -i input.csv -o output.csv ersilia close From efaf8193f3f1285cf4442cb1b73db94ad548240b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 1 Oct 2023 00:25:00 +0000 Subject: [PATCH 03/24] Bump GrantBirki/json-yaml-validate from 2.3.0 to 2.3.1 Bumps [GrantBirki/json-yaml-validate](https://github.com/grantbirki/json-yaml-validate) from 2.3.0 to 2.3.1. - [Release notes](https://github.com/grantbirki/json-yaml-validate/releases) - [Commits](https://github.com/grantbirki/json-yaml-validate/compare/1652fde01b1be71dfa7131148819e67639792673...3add42f5fa8bfff04a3fe664d27a316736257ef1) --- updated-dependencies: - dependency-name: GrantBirki/json-yaml-validate dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- .github/workflows/json-check.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/json-check.yml b/.github/workflows/json-check.yml index 2baa7172d..4bee99523 100644 --- a/.github/workflows/json-check.yml +++ b/.github/workflows/json-check.yml @@ -18,7 +18,7 @@ jobs: uses: actions/checkout@3df4ab11eba7bda6032a0b82a6bb43b11571feac # pin@v3.5.3 - name: json syntax check - uses: GrantBirki/json-yaml-validate@1652fde01b1be71dfa7131148819e67639792673 # pin@v2.3.0 + uses: GrantBirki/json-yaml-validate@3add42f5fa8bfff04a3fe664d27a316736257ef1 # pin@v2.3.1 with: exclude_file: ".github/config/exclude.txt" # .gitignore style file for exclusions comment: "true" # allow PR comments with error messages From 55c8d8f1461240f489de86031610f1ffa333bf07 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 1 Oct 2023 00:25:04 +0000 Subject: [PATCH 04/24] Bump docker/setup-buildx-action from 2 to 3 Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2 to 3. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](https://github.com/docker/setup-buildx-action/compare/v2...v3) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/ersilia-base-image-to-dockerhub.yml | 2 +- .github/workflows/ersilia-installer-to-dockerhub.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ersilia-base-image-to-dockerhub.yml b/.github/workflows/ersilia-base-image-to-dockerhub.yml index 6b374e28b..1a117937b 100644 --- a/.github/workflows/ersilia-base-image-to-dockerhub.yml +++ b/.github/workflows/ersilia-base-image-to-dockerhub.yml @@ -16,7 +16,7 @@ jobs: # 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 diff --git a/.github/workflows/ersilia-installer-to-dockerhub.yml b/.github/workflows/ersilia-installer-to-dockerhub.yml index a4d455361..617f0d3cf 100644 --- a/.github/workflows/ersilia-installer-to-dockerhub.yml +++ b/.github/workflows/ersilia-installer-to-dockerhub.yml @@ -18,7 +18,7 @@ jobs: # 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 From 63a743751f2605b108422cb47857234259bb23a9 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 1 Oct 2023 00:25:10 +0000 Subject: [PATCH 05/24] Bump actions/checkout from 4.0.0 to 4.1.0 Bumps [actions/checkout](https://github.com/actions/checkout) from 4.0.0 to 4.1.0. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/3df4ab11eba7bda6032a0b82a6bb43b11571feac...8ade135a41bc03ea155e62e844d188df1ea18608) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- .github/workflows/approve-dispatch.yml | 4 ++-- .github/workflows/install.yml | 6 +++--- .github/workflows/json-check.yml | 2 +- .github/workflows/pr_check.yml | 2 +- .github/workflows/predict-model-input.yml | 2 +- .github/workflows/predict-model.yml | 2 +- .github/workflows/python-publish.yml | 2 +- .github/workflows/quick-manual-model-test.yml | 2 +- .github/workflows/tag-to-version.yml | 2 +- .github/workflows/test-colab.yml | 2 +- .github/workflows/test.yml | 2 +- .github/workflows/write_secrets.yml | 2 +- 12 files changed, 15 insertions(+), 15 deletions(-) diff --git a/.github/workflows/approve-dispatch.yml b/.github/workflows/approve-dispatch.yml index f4928ca91..b659abd48 100644 --- a/.github/workflows/approve-dispatch.yml +++ b/.github/workflows/approve-dispatch.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout - uses: actions/checkout@3df4ab11eba7bda6032a0b82a6bb43b11571feac # pin@v3.5.3 + uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # pin@v3.5.3 # parse the issue body from free form text to a structured JSON object - name: parse issue @@ -81,7 +81,7 @@ jobs: # upload git-lfs object - name: checkout persist credentials - uses: actions/checkout@3df4ab11eba7bda6032a0b82a6bb43b11571feac # pin@v3.5.3 + uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # pin@v3.5.3 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/install.yml b/.github/workflows/install.yml index b24bfb3ab..1f69d81bf 100644 --- 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 # pin@v3.5.3 + - uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # pin@v3.5.3 - 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 index 2baa7172d..6e7d6fe7d 100644 --- a/.github/workflows/json-check.yml +++ b/.github/workflows/json-check.yml @@ -15,7 +15,7 @@ jobs: runs-on: ubuntu-latest steps: - name: checkout - uses: actions/checkout@3df4ab11eba7bda6032a0b82a6bb43b11571feac # pin@v3.5.3 + uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # pin@v3.5.3 - name: json syntax check uses: GrantBirki/json-yaml-validate@1652fde01b1be71dfa7131148819e67639792673 # pin@v2.3.0 diff --git a/.github/workflows/pr_check.yml b/.github/workflows/pr_check.yml index 589f52219..7c0972a31 100644 --- 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 # pin@v3.5.3 + - uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # pin@v3.5.3 - 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 index a49bdbf7a..54e58aa3b 100644 --- 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 # pin@v3.5.3 + - uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # pin@v3.5.3 - name: Add conda to system path run: echo $CONDA/bin >> $GITHUB_PATH diff --git a/.github/workflows/predict-model.yml b/.github/workflows/predict-model.yml index db25d6fcb..b22a33558 100644 --- 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 # pin@v3.5.3 + - uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # pin@v3.5.3 - 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 index 3a34b1822..83a857373 100644 --- 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 # pin@v3.5.3 + - uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # pin@v3.5.3 - name: Set up Python uses: actions/setup-python@61a6322f88396a6271a6ee3565807d608ecaddd1 # pin@v4.7.0 diff --git a/.github/workflows/quick-manual-model-test.yml b/.github/workflows/quick-manual-model-test.yml index 9c1c062ce..61e2dbdae 100644 --- 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 # pin@v3.5.3 + - uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # pin@v3.5.3 - name: Add conda to system path run: echo $CONDA/bin >> $GITHUB_PATH diff --git a/.github/workflows/tag-to-version.yml b/.github/workflows/tag-to-version.yml index 58b68168c..f24c20ac3 100644 --- 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 # pin@v3.5.3 + uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # pin@v3.5.3 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 index 0b4e59dc7..feda6a9df 100644 --- 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 # pin@v3.5.3 + - uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # pin@v3.5.3 - name: Add conda to system path run: echo $CONDA/bin >> $GITHUB_PATH diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 8b9fd182e..562aa30d7 100644 --- 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 # pin@v3.5.3 + - uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # pin@v3.5.3 - 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 index 98eacc7a2..945f9189e 100644 --- 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 # pin@v3.5.3 + - uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # pin@v3.5.3 # Write json file - name: Write secrets to json file From b012b9a3896cc363bbd61b744cb640ade1e17923 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 1 Oct 2023 00:25:13 +0000 Subject: [PATCH 06/24] Bump docker/setup-qemu-action from 2 to 3 Bumps [docker/setup-qemu-action](https://github.com/docker/setup-qemu-action) from 2 to 3. - [Release notes](https://github.com/docker/setup-qemu-action/releases) - [Commits](https://github.com/docker/setup-qemu-action/compare/v2...v3) --- updated-dependencies: - dependency-name: docker/setup-qemu-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/ersilia-base-image-to-dockerhub.yml | 2 +- .github/workflows/ersilia-installer-to-dockerhub.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ersilia-base-image-to-dockerhub.yml b/.github/workflows/ersilia-base-image-to-dockerhub.yml index 6b374e28b..18c599c71 100644 --- a/.github/workflows/ersilia-base-image-to-dockerhub.yml +++ b/.github/workflows/ersilia-base-image-to-dockerhub.yml @@ -11,7 +11,7 @@ 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 diff --git a/.github/workflows/ersilia-installer-to-dockerhub.yml b/.github/workflows/ersilia-installer-to-dockerhub.yml index a4d455361..71f0bfdc2 100644 --- a/.github/workflows/ersilia-installer-to-dockerhub.yml +++ b/.github/workflows/ersilia-installer-to-dockerhub.yml @@ -13,7 +13,7 @@ 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 From ae5c76fc1e1df97b1a0ecd58650ea379d94cbbf7 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 1 Oct 2023 00:25:16 +0000 Subject: [PATCH 07/24] Bump GrantBirki/issue-template-parser from 6.1.0 to 6.1.1 Bumps [GrantBirki/issue-template-parser](https://github.com/grantbirki/issue-template-parser) from 6.1.0 to 6.1.1. - [Release notes](https://github.com/grantbirki/issue-template-parser/releases) - [Commits](https://github.com/grantbirki/issue-template-parser/compare/v6.1.0...v6.1.1) --- updated-dependencies: - dependency-name: GrantBirki/issue-template-parser dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- .github/workflows/approve-dispatch.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/approve-dispatch.yml b/.github/workflows/approve-dispatch.yml index f4928ca91..30ab1872a 100644 --- a/.github/workflows/approve-dispatch.yml +++ b/.github/workflows/approve-dispatch.yml @@ -17,7 +17,7 @@ jobs: # parse the issue body from free form text to a structured JSON object - name: parse issue - uses: GrantBirki/issue-template-parser@v6.1.0 + uses: GrantBirki/issue-template-parser@v6.1.1 id: issue-parser with: body: ${{ github.event.client_payload.github.payload.issue.body }} From c06fbf80eb8afe45ac87e152e9d8c10cf440ba25 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 1 Oct 2023 00:25:21 +0000 Subject: [PATCH 08/24] Bump docker/metadata-action from 4 to 5 Bumps [docker/metadata-action](https://github.com/docker/metadata-action) from 4 to 5. - [Release notes](https://github.com/docker/metadata-action/releases) - [Upgrade guide](https://github.com/docker/metadata-action/blob/master/UPGRADE.md) - [Commits](https://github.com/docker/metadata-action/compare/v4...v5) --- updated-dependencies: - dependency-name: docker/metadata-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/ersilia-base-image-to-dockerhub.yml | 2 +- .github/workflows/ersilia-installer-to-dockerhub.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ersilia-base-image-to-dockerhub.yml b/.github/workflows/ersilia-base-image-to-dockerhub.yml index 6b374e28b..81fce1d3f 100644 --- a/.github/workflows/ersilia-base-image-to-dockerhub.yml +++ b/.github/workflows/ersilia-base-image-to-dockerhub.yml @@ -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: | diff --git a/.github/workflows/ersilia-installer-to-dockerhub.yml b/.github/workflows/ersilia-installer-to-dockerhub.yml index a4d455361..9c0352765 100644 --- a/.github/workflows/ersilia-installer-to-dockerhub.yml +++ b/.github/workflows/ersilia-installer-to-dockerhub.yml @@ -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: | From 5831696e14f72f9957538e990f63bf2a9e4028c5 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 1 Oct 2023 00:25:24 +0000 Subject: [PATCH 09/24] Bump actions/upload-artifact from 3.1.2 to 3.1.3 Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 3.1.2 to 3.1.3. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/0b7f8abb1508181956e8e162db84b466c27e18ce...a8a3f3ad30e3422c9c7b888a15615d19a852ae32) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- .github/workflows/quick-manual-model-test.yml | 2 +- .github/workflows/test-colab.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/quick-manual-model-test.yml b/.github/workflows/quick-manual-model-test.yml index 9c1c062ce..660342e03 100644 --- a/.github/workflows/quick-manual-model-test.yml +++ b/.github/workflows/quick-manual-model-test.yml @@ -58,7 +58,7 @@ jobs: - name: Upload log output if: ${{ failure() }} - uses: actions/upload-artifact@0b7f8abb1508181956e8e162db84b466c27e18ce # pin@v3.1.2 + uses: actions/upload-artifact@a8a3f3ad30e3422c9c7b888a15615d19a852ae32 # pin@v3.1.3 with: name: ersilia-predict-logs path: /home/runner/eos/console.log diff --git a/.github/workflows/test-colab.yml b/.github/workflows/test-colab.yml index 0b4e59dc7..6d9c2bc1e 100644 --- a/.github/workflows/test-colab.yml +++ b/.github/workflows/test-colab.yml @@ -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 # pin@v3.1.2 + uses: actions/upload-artifact@a8a3f3ad30e3422c9c7b888a15615d19a852ae32 # pin@v3.1.3 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 # pin@v3.1.2 + uses: actions/upload-artifact@a8a3f3ad30e3422c9c7b888a15615d19a852ae32 # pin@v3.1.3 with: name: output-python-api.ipynb path: notebooks/output-python-api.ipynb From 8db3246b25e39c385581c690ea36491a54748563 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 1 Oct 2023 00:25:28 +0000 Subject: [PATCH 10/24] Bump docker/build-push-action from 4 to 5 Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4 to 5. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](https://github.com/docker/build-push-action/compare/v4...v5) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/ersilia-base-image-to-dockerhub.yml | 2 +- .github/workflows/ersilia-installer-to-dockerhub.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ersilia-base-image-to-dockerhub.yml b/.github/workflows/ersilia-base-image-to-dockerhub.yml index 6b374e28b..07e231366 100644 --- a/.github/workflows/ersilia-base-image-to-dockerhub.yml +++ b/.github/workflows/ersilia-base-image-to-dockerhub.yml @@ -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 index a4d455361..12308912f 100644 --- a/.github/workflows/ersilia-installer-to-dockerhub.yml +++ b/.github/workflows/ersilia-installer-to-dockerhub.yml @@ -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 From 7d366f10172b5e4a673a25d0447963a4f4bdc355 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 1 Oct 2023 00:25:31 +0000 Subject: [PATCH 11/24] Bump docker/login-action from 2 to 3 Bumps [docker/login-action](https://github.com/docker/login-action) from 2 to 3. - [Release notes](https://github.com/docker/login-action/releases) - [Commits](https://github.com/docker/login-action/compare/v2...v3) --- updated-dependencies: - dependency-name: docker/login-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/ersilia-base-image-to-dockerhub.yml | 2 +- .github/workflows/ersilia-installer-to-dockerhub.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ersilia-base-image-to-dockerhub.yml b/.github/workflows/ersilia-base-image-to-dockerhub.yml index 6b374e28b..5d6236d4c 100644 --- a/.github/workflows/ersilia-base-image-to-dockerhub.yml +++ b/.github/workflows/ersilia-base-image-to-dockerhub.yml @@ -21,7 +21,7 @@ jobs: # 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 }} diff --git a/.github/workflows/ersilia-installer-to-dockerhub.yml b/.github/workflows/ersilia-installer-to-dockerhub.yml index a4d455361..e6e901a9f 100644 --- a/.github/workflows/ersilia-installer-to-dockerhub.yml +++ b/.github/workflows/ersilia-installer-to-dockerhub.yml @@ -23,7 +23,7 @@ jobs: # 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 }} From 480ad0fdacaf1eb7aa1bbe048c092d2ba584fdb8 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 1 Oct 2023 00:25:35 +0000 Subject: [PATCH 12/24] Bump GrantBirki/comment from 2.0.6 to 2.0.7 Bumps [GrantBirki/comment](https://github.com/grantbirki/comment) from 2.0.6 to 2.0.7. - [Release notes](https://github.com/grantbirki/comment/releases) - [Commits](https://github.com/grantbirki/comment/compare/eab1bc94aa728cf526dcd6639bfd067512d4a5cb...e6bf4bc177996c9572b4ddb98b25eb1a80f9abc9) --- updated-dependencies: - dependency-name: GrantBirki/comment dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- .github/workflows/approve-dispatch.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/approve-dispatch.yml b/.github/workflows/approve-dispatch.yml index f4928ca91..6c71e5d67 100644 --- a/.github/workflows/approve-dispatch.yml +++ b/.github/workflows/approve-dispatch.yml @@ -154,7 +154,7 @@ jobs: # comment on the issue comment with further instructions for the user - name: comment - uses: GrantBirki/comment@eab1bc94aa728cf526dcd6639bfd067512d4a5cb # pin@v2.0.6 + uses: GrantBirki/comment@e6bf4bc177996c9572b4ddb98b25eb1a80f9abc9 # pin@v2.0.7 with: issue-number: ${{ github.event.client_payload.github.payload.issue.number }} file: .github/templates/new-model.md From 39ca36464c0e677c511857e09716221246902c6d Mon Sep 17 00:00:00 2001 From: Miquel Duran-Frigola Date: Thu, 5 Oct 2023 06:33:34 +0200 Subject: [PATCH 13/24] Update predict-model-input.yml --- .github/workflows/predict-model-input.yml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/.github/workflows/predict-model-input.yml b/.github/workflows/predict-model-input.yml index 79c9e4425..d7be55a36 100644 --- a/.github/workflows/predict-model-input.yml +++ b/.github/workflows/predict-model-input.yml @@ -44,15 +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 succesfully fetched and served" + 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 From 40710230f675f45c93c6d330d498125c738935ae Mon Sep 17 00:00:00 2001 From: Miquel Duran-Frigola Date: Thu, 5 Oct 2023 06:45:22 +0200 Subject: [PATCH 14/24] bugfix circleci --- .circleci/config.yml | 3 ++- README.md | 7 +++++-- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 6c2be03ad..eafde76b2 100644 --- 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: | diff --git a/README.md b/README.md index 3648c82a8..abc1ecbae 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@
-# 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/) From 89eb6e24f154d8514cf29b88a87649b7320c301c Mon Sep 17 00:00:00 2001 From: Miquel Duran-Frigola Date: Thu, 5 Oct 2023 06:55:06 +0200 Subject: [PATCH 15/24] remove pytest since it is redundant --- .circleci/config.yml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index eafde76b2..18a0563ff 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -64,12 +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 From 4ca4fdd4dab27ebf818375679ce8f48669a7e144 Mon Sep 17 00:00:00 2001 From: Miquel Duran-Frigola Date: Thu, 5 Oct 2023 07:05:12 +0200 Subject: [PATCH 16/24] added setuptools --- .circleci/config.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.circleci/config.yml b/.circleci/config.yml index 18a0563ff..205a7a570 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -74,6 +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: From 4bc228c0d6942d2a486e78a1bc0ab432f5eae5ea Mon Sep 17 00:00:00 2001 From: Anthony Cui Date: Sat, 7 Oct 2023 17:37:03 -0400 Subject: [PATCH 17/24] Fix file reading error --- ersilia/io/readers/file.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ersilia/io/readers/file.py b/ersilia/io/readers/file.py index 3b0202a25..6bc3156ea 100644 --- a/ersilia/io/readers/file.py +++ b/ersilia/io/readers/file.py @@ -318,7 +318,7 @@ def read_input_columns(self): h = next(reader) else: h = None - if len(h) == 1: + if h is not None and len(h) == 1: for l in reader: l = self._column_delimiter.join(l) R += [[l]] From 10562e571a94dbb3d2400c6b35530f6228e10c77 Mon Sep 17 00:00:00 2001 From: Anthony Cui <35975809+AC-Dap@users.noreply.github.com> Date: Sat, 7 Oct 2023 18:24:12 -0400 Subject: [PATCH 18/24] Create black-code-formatter.yml --- .github/workflows/black-code-formatter.yml | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 .github/workflows/black-code-formatter.yml diff --git a/.github/workflows/black-code-formatter.yml b/.github/workflows/black-code-formatter.yml new file mode 100644 index 000000000..96dc0673b --- /dev/null +++ b/.github/workflows/black-code-formatter.yml @@ -0,0 +1,13 @@ +name: Python Black Linter + +on: [push, pull_request] + +jobs: + lint: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + - uses: psf/black@stable + with: + options: "--check" + src: "./ersilia" From f265b5fcca0530adbbfa90cebdf65b6c36f01125 Mon Sep 17 00:00:00 2001 From: Anthony Cui Date: Sun, 8 Oct 2023 01:16:20 -0400 Subject: [PATCH 19/24] Fix linting issues --- ersilia/cli/commands/info.py | 6 ++++-- ersilia/cli/commands/run.py | 11 +++++++++-- ersilia/core/model.py | 9 ++++++--- ersilia/core/tracking.py | 2 +- ersilia/hub/content/information.py | 10 +++++----- 5 files changed, 25 insertions(+), 13 deletions(-) diff --git a/ersilia/cli/commands/info.py b/ersilia/cli/commands/info.py index 9c4f95b69..4815b5ead 100644 --- 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() \ No newline at end of file + InformationDisplayer(info).echo() diff --git a/ersilia/cli/commands/run.py b/ersilia/cli/commands/run.py index db813cc5d..025f1c75f 100644 --- 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: diff --git a/ersilia/core/model.py b/ersilia/core/model.py index 6ec580fec..30500beef 100644 --- a/ersilia/core/model.py +++ b/ersilia/core/model.py @@ -48,7 +48,7 @@ def __init__( fetch_if_not_available=True, preferred_port=None, log_runs=True, - track_runs=False + track_runs=False, ): ErsiliaBase.__init__( self, config_json=config_json, credentials_json=credentials_json @@ -148,7 +148,8 @@ def is_valid(self): def _set_api(self, api_name): # Don't want to override apis we explicitly write - if hasattr(self, api_name): return + if hasattr(self, api_name): + return def _method(input=None, output=None, batch_size=DEFAULT_BATCH_SIZE): return self.api(api_name, input, output, batch_size) @@ -412,7 +413,9 @@ def close(self): def get_apis(self): return self.autoservice.get_apis() - def run(self, input=None, output=None, batch_size=DEFAULT_BATCH_SIZE, track_run=False): + def run( + self, input=None, output=None, batch_size=DEFAULT_BATCH_SIZE, track_run=False + ): api_name = self.get_apis()[0] result = self.api( api_name=api_name, input=input, output=output, batch_size=batch_size diff --git a/ersilia/core/tracking.py b/ersilia/core/tracking.py index 25da8f774..0a9bfaed7 100644 --- a/ersilia/core/tracking.py +++ b/ersilia/core/tracking.py @@ -14,4 +14,4 @@ def track(self, input, result, meta): print("Run input file:", input) print("Run output file:", result) - print("Model metadata:", meta) \ No newline at end of file + print("Model metadata:", meta) diff --git a/ersilia/hub/content/information.py b/ersilia/hub/content/information.py index 5acb20b62..61f6eff64 100644 --- a/ersilia/hub/content/information.py +++ b/ersilia/hub/content/information.py @@ -1,5 +1,6 @@ import os import json + try: import emoji except: @@ -94,21 +95,20 @@ def get(self): "card": self._get_card(), } return data - -class InformationDisplayer(ErsiliaBase): +class InformationDisplayer(ErsiliaBase): def __init__(self, info_data, config_json=None): ErsiliaBase.__init__(self, config_json=config_json, credentials_json=None) self.info_data = info_data self.logger.debug(self.info_data) - + @staticmethod def _echo(text, **styles): if emoji is not None: text = emoji.emojize(text) return click.echo(click.style(text, **styles)) - + def _description_info(self): color = "blue" card = self.info_data["card"] @@ -166,4 +166,4 @@ def echo(self): self._code_info() self._docker_info() text = "For more information, please visit https://ersilia.io/model-hub" - self._echo(text, fg="black") \ No newline at end of file + self._echo(text, fg="black") From 67991aef9f4d86b54a553b599d129e6c3f389432 Mon Sep 17 00:00:00 2001 From: Anthony Cui Date: Sun, 8 Oct 2023 13:29:59 -0400 Subject: [PATCH 20/24] Add Github lint action when comment is made --- .github/workflows/black-code-formatter.yml | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/.github/workflows/black-code-formatter.yml b/.github/workflows/black-code-formatter.yml index 96dc0673b..2b63149f6 100644 --- a/.github/workflows/black-code-formatter.yml +++ b/.github/workflows/black-code-formatter.yml @@ -1,6 +1,6 @@ name: Python Black Linter -on: [push, pull_request] +on: [ push, pull_request ] jobs: lint: @@ -11,3 +11,19 @@ jobs: 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 From a8d754d8ceddde2727a4dc31a0984dc3a31fe640 Mon Sep 17 00:00:00 2001 From: Anthony Cui Date: Sun, 8 Oct 2023 13:36:49 -0400 Subject: [PATCH 21/24] Test bad code formatting --- ersilia/core/tracking.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/ersilia/core/tracking.py b/ersilia/core/tracking.py index 0a9bfaed7..8212d9adb 100644 --- a/ersilia/core/tracking.py +++ b/ersilia/core/tracking.py @@ -5,7 +5,6 @@ class RunTracker: NOTE: Currently, the Splunk connection is not set up. For now, we will print tracking results to the console. """ - def track(self, input, result, meta): """ Tracks the results after a model run. @@ -14,4 +13,4 @@ def track(self, input, result, meta): print("Run input file:", input) print("Run output file:", result) - print("Model metadata:", meta) + print("Model metadata:", meta) \ No newline at end of file From defadcbb44e12bb9263bf538b47b16a04fd18043 Mon Sep 17 00:00:00 2001 From: Anthony Cui Date: Sun, 8 Oct 2023 14:03:23 -0400 Subject: [PATCH 22/24] Add "issue_comment" as possible workflow trigger --- .github/workflows/black-code-formatter.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/black-code-formatter.yml b/.github/workflows/black-code-formatter.yml index 2b63149f6..61da7f255 100644 --- a/.github/workflows/black-code-formatter.yml +++ b/.github/workflows/black-code-formatter.yml @@ -1,9 +1,10 @@ name: Python Black Linter -on: [ push, pull_request ] +on: [ push, pull_request, issue_comment ] 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 From e5905ae87c886c467d5ca39b990bd2464ccdb78e Mon Sep 17 00:00:00 2001 From: Anthony Cui <35975809+AC-Dap@users.noreply.github.com> Date: Sun, 8 Oct 2023 14:12:40 -0400 Subject: [PATCH 23/24] Fix YAML syntax --- .github/workflows/black-code-formatter.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/black-code-formatter.yml b/.github/workflows/black-code-formatter.yml index 61da7f255..692a06d5b 100644 --- a/.github/workflows/black-code-formatter.yml +++ b/.github/workflows/black-code-formatter.yml @@ -4,7 +4,7 @@ on: [ push, pull_request, issue_comment ] jobs: lint: - if: !contains(github.event_name, 'issue_comment') # Don't want to trigger on comments + if: ${{ !contains(github.event_name, 'issue_comment') }} # Don't want to trigger on comments runs-on: ubuntu-latest steps: - uses: actions/checkout@v3 @@ -13,7 +13,7 @@ jobs: options: "--check" src: "./ersilia" comment-lint: - if: github.event.issue.pull_request && contains(github.event.comment.body, '✨') + 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 From 07b307cbd9a673d45e73a378e3ac4456cf96a932 Mon Sep 17 00:00:00 2001 From: Anthony Cui Date: Sun, 8 Oct 2023 14:23:47 -0400 Subject: [PATCH 24/24] Be more specific with event triggers --- .github/workflows/black-code-formatter.yml | 6 +++++- ersilia/core/tracking.py | 3 ++- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/.github/workflows/black-code-formatter.yml b/.github/workflows/black-code-formatter.yml index 692a06d5b..16f625f90 100644 --- a/.github/workflows/black-code-formatter.yml +++ b/.github/workflows/black-code-formatter.yml @@ -1,6 +1,10 @@ name: Python Black Linter -on: [ push, pull_request, issue_comment ] +on: + push: + pull_request: + issue_comment: + types: [ created, edited ] jobs: lint: diff --git a/ersilia/core/tracking.py b/ersilia/core/tracking.py index 8212d9adb..0a9bfaed7 100644 --- a/ersilia/core/tracking.py +++ b/ersilia/core/tracking.py @@ -5,6 +5,7 @@ class RunTracker: NOTE: Currently, the Splunk connection is not set up. For now, we will print tracking results to the console. """ + def track(self, input, result, meta): """ Tracks the results after a model run. @@ -13,4 +14,4 @@ def track(self, input, result, meta): print("Run input file:", input) print("Run output file:", result) - print("Model metadata:", meta) \ No newline at end of file + print("Model metadata:", meta)