From 7d332d06874ced26fc8195635b126f2658078099 Mon Sep 17 00:00:00 2001
From: Chiara Rasi <rasi.chiara@gmacil.com>
Date: Thu, 21 Nov 2024 11:51:11 +0100
Subject: [PATCH] Updated actions using the latest base images and to run using
 Python 3.9

---
 .github/workflows/black.yml                | 4 ++--
 .github/workflows/dockerhub_stage_push.yml | 4 ++--
 .github/workflows/keep_changelog.yml       | 2 +-
 .github/workflows/lint.yml                 | 4 ++--
 .github/workflows/test_n_coverage.yml      | 6 +++---
 .github/workflows/vulture.yml              | 4 ++--
 CHANGELOG.md                               | 1 +
 README.md                                  | 2 +-
 8 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml
index eb99c11..2d8ddfd 100644
--- a/.github/workflows/black.yml
+++ b/.github/workflows/black.yml
@@ -9,9 +9,9 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
       - name: install black
         run: |
           pip install black==22.3.0
diff --git a/.github/workflows/dockerhub_stage_push.yml b/.github/workflows/dockerhub_stage_push.yml
index bbf6e59..95777e5 100644
--- a/.github/workflows/dockerhub_stage_push.yml
+++ b/.github/workflows/dockerhub_stage_push.yml
@@ -15,7 +15,7 @@ jobs:
 
      - name: Get branch name
        id: branch-name
-       uses: tj-actions/branch-names@v7
+       uses: tj-actions/branch-names@v8
 
      - name: Login to Docker Hub
        uses: docker/login-action@v3
@@ -29,7 +29,7 @@ jobs:
 
      - name: Build and push
        if: steps.branch-name.outputs.is_default == 'false'
-       uses: docker/build-push-action@v5
+       uses: docker/build-push-action@v6
        with:
          context: ./
          file: ./Dockerfile
diff --git a/.github/workflows/keep_changelog.yml b/.github/workflows/keep_changelog.yml
index 7711de4..1d56d9f 100644
--- a/.github/workflows/keep_changelog.yml
+++ b/.github/workflows/keep_changelog.yml
@@ -8,7 +8,7 @@ jobs:
   changelog:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - uses: dangoslen/changelog-enforcer@v3
       with:
         changeLogPath: 'CHANGELOG.md'
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index bdd2605..6d2321e 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -9,9 +9,9 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@master
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
       - name: install flake8
         run: |
           pip install flake8
diff --git a/.github/workflows/test_n_coverage.yml b/.github/workflows/test_n_coverage.yml
index e8152ae..f0162a1 100644
--- a/.github/workflows/test_n_coverage.yml
+++ b/.github/workflows/test_n_coverage.yml
@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.8' ]
+        python-version: [ '3.9' ]
     steps:
       - uses: actions/checkout@v4
       - name: Install poetry
@@ -18,7 +18,7 @@ jobs:
           rm install-poetry.py
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'poetry'
@@ -37,7 +37,7 @@ jobs:
         run: poetry run pytest --cov=./ --cov-report=xml
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           flags: unittests
           files: ./coverage.xml
diff --git a/.github/workflows/vulture.yml b/.github/workflows/vulture.yml
index 67e0b08..5d6e6fb 100644
--- a/.github/workflows/vulture.yml
+++ b/.github/workflows/vulture.yml
@@ -13,12 +13,12 @@ jobs:
 
       - name: Find changed Python files
         id: files
-        uses: Ana06/get-changed-files@v2.0.0
+        uses: Ana06/get-changed-files@v2
         with:
           filter: "*.py"
 
       - name: Scavenge
-        uses: anaynayak/python-vulture-action@v1.0
+        uses: anaynayak/python-vulture-action@v1
         id: vulture
         with:
           vulture-args: --min-confidence 80 ${{steps.files.outputs.all}}
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 37b51e8..47c59bc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,7 @@
 - Updated API submission schema to the latest available on `ncbi/clinvar` GitHub pages
 - Modified the json submission example to use one from the ClinVar GitHib repo (`sample_clinical_significance_hgvs_submission.json`)
 - Removed the example of an old json submission (before 2022-11-21) 
+- Updated actions using the latest base images and to run using Python 3.9
 ### Fixed
 - Updated issue templates
 - Updated a number of libraries to address all current security advisories
diff --git a/README.md b/README.md
index 22de14f..2fcf06c 100644
--- a/README.md
+++ b/README.md
@@ -37,7 +37,7 @@ The server will be running and accepting requests sent from outside the containe
 
 ## Installing the application on a local conda environment
 
-Given a conda environment sontaining python 3.8 and [poetry](https://github.com/python-poetry/poetry), clone the repository from Github with the following command:
+Given a conda environment containing Python 3.9 and [poetry](https://github.com/python-poetry/poetry), clone the repository from Github with the following command:
 
 ```
 git clone https://github.com/Clinical-Genomics/preClinVar.git