Merge branch 'v4.8.0-rc-dev'

Author: BryanFauble

.github/pull_request_template.md

@@ -0,0 +1,25 @@
+# **Problem:**
+
+- Describe the specific technical problem that this PR solves.
+- Include  details such as:
+    - How you reproduced the problem
+    - What code is affected
+    - Any relevant background information
+
+# **Solution:**
+
+- Describe the specific technical solution that this PR provides.
+- Include details such as:
+    - How you debugged the problem
+    - Why you chose this solution
+    - Does the solution make any impact beyond the immediate problem
+    - Any necessary technical debt incurred
+    - Any important design decisions/links to design documentation (if applicable)
+
+# **Testing:**
+
+- Describe any testing that was performed to validate the solution.
+- Include details such as:
+    - How you tested the solution
+    - Any relevant test results (Do not include any test results that may contain sensitive information)
+    - Any automated tests that were added to the codebase

.github/workflows/build.yml

@@ -27,6 +27,12 @@ on:
     types:
       - 'published'
 
+# Cancel any previous runs of this workflow that are still in progress.
+# This is to avoid running the same tests multiple times concurrently.
+concurrency:
+  group: ci-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
 
   pre-commit:
@@ -35,21 +41,20 @@ jobs:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
       with:
-        python-version: '3.12'
+        python-version: '3.13'
     - uses: pre-commit/[email protected]
 
-
   # run unit (and integration tests if account secrets available) on our build matrix
   test:
     needs: [pre-commit]
 
     strategy:
       matrix:
-        os: [ubuntu-20.04, macos-13, windows-2022]
+        os: [ubuntu-22.04, macos-13, windows-2022]
 
         # if changing the below change the run-integration-tests versions and the check-deploy versions
         # Make sure that we are running the integration tests on the first and last versions of the matrix
-        python: ['3.9', '3.10', '3.11', '3.12']
+        python: ['3.9', '3.10', '3.11', '3.12', '3.13']
 
     runs-on: ${{ matrix.os }}
 
@@ -78,7 +83,7 @@ jobs:
           path: |
             ${{ steps.get-dependencies.outputs.site_packages_loc }}
             ${{ steps.get-dependencies.outputs.site_bin_dir }}
-          key: ${{ runner.os }}-${{ matrix.python }}-build-${{ env.cache-name }}-${{ hashFiles('setup.py') }}-v20
+          key: ${{ runner.os }}-${{ matrix.python }}-build-${{ env.cache-name }}-${{ hashFiles('setup.py') }}-v22
 
       - name: Install py-dependencies
         if: steps.cache-dependencies.outputs.cache-hit != 'true'
@@ -101,7 +106,7 @@ jobs:
           pytest -sv --cov-append --cov=. --cov-report xml tests/unit
       - name: Check for Secret availability
         id: secret-check
-        if: ${{ contains(fromJSON('["3.9"]'), matrix.python) || contains(fromJSON('["3.12"]'), matrix.python) }}
+        if: ${{ contains(fromJSON('["3.9"]'), matrix.python) || contains(fromJSON('["3.13"]'), matrix.python) }}
         # perform secret check & put boolean result as an output
         shell: bash
         run: |
@@ -160,7 +165,7 @@ jobs:
         shell: bash
 
         # keep versions consistent with the first and last from the strategy matrix
-        if: ${{ (contains(fromJSON('["3.9"]'), matrix.python) || contains(fromJSON('["3.12"]'), matrix.python)) && steps.secret-check.outputs.secrets_available == 'true'}}
+        if: ${{ (contains(fromJSON('["3.9"]'), matrix.python) || contains(fromJSON('["3.13"]'), matrix.python)) && steps.secret-check.outputs.secrets_available == 'true'}}
         run: |
           # decrypt the encrypted test synapse configuration
           openssl aes-256-cbc -K ${{ secrets.encrypted_d17283647768_key }} -iv ${{ secrets.encrypted_d17283647768_iv }} -in test.synapseConfig.enc -out test.synapseConfig -d
@@ -207,7 +212,7 @@ jobs:
       - name: Upload coverage report
         id: upload_coverage_report
         uses: actions/upload-artifact@v4
-        if: ${{ contains(fromJSON('["3.12"]'), matrix.python) && contains(fromJSON('["ubuntu-20.04"]'), matrix.os)}}
+        if: ${{ contains(fromJSON('["3.13"]'), matrix.python) && contains(fromJSON('["ubuntu-22.04"]'), matrix.os)}}
         with:
           name: coverage-report
           path: coverage.xml
@@ -216,7 +221,7 @@ jobs:
     needs: [test]
     if: ${{ always() && !cancelled()}}
     name: SonarCloud
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v4
         with:
@@ -251,7 +256,7 @@ jobs:
   package:
     needs: [test,pre-commit]
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     if: github.event_name == 'release'
 
@@ -399,10 +404,10 @@ jobs:
 
     strategy:
       matrix:
-        os: [ubuntu-20.04, macos-13, windows-2022]
+        os: [ubuntu-24.04, macos-13, windows-2022]
 
         # python versions should be consistent with the strategy matrix and the runs-integration-tests versions
-        python: ['3.9', '3.10', '3.11', '3.12']
+        python: ['3.9', '3.10', '3.11', '3.12', '3.13']
 
     runs-on: ${{ matrix.os }}
 

.readthedocs.yaml

@@ -6,9 +6,10 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
-    python: "3.9"
+    # alias for the latest 3.x version available on Read the Docs
+    python: "3"
 
 mkdocs:
   configuration: mkdocs.yml
@@ -17,3 +18,10 @@ mkdocs:
 python:
   install:
   - requirements: docs/requirements.txt
+
+# See https://docs.readthedocs.com/platform/stable/config-file/v2.html#search for more options
+search:
+  ranking:
+    reference/*: -3
+    reference/experimental/*: -2
+    reference/experimental/sync/*: -1

CONTRIBUTING.md

@@ -93,7 +93,7 @@ copied to forks).
 #### Installing the Python Client in a virtual environment with pipenv
 Perform the following one-time steps to set up your local environment.
 
-1. This package uses Python, if you have not already, please install [pyenv](https://github.com/pyenv/pyenv#installation) to manage your Python versions. Versions supported by this package are all versions >=3.9 and <=3.12. If you do not install `pyenv` make sure that Python and `pip` are installed correctly and have been added to your PATH by running `python3 --version` and `pip3 --version`. If your installation was successful, your terminal will return the versions of Python and `pip` that you installed.  **Note**: If you have `pyenv` it will install a specific version of Python for you.
+1. This package uses Python, if you have not already, please install [pyenv](https://github.com/pyenv/pyenv#installation) to manage your Python versions. Versions supported by this package are all versions >=3.9 and <=3.13. If you do not install `pyenv` make sure that Python and `pip` are installed correctly and have been added to your PATH by running `python3 --version` and `pip3 --version`. If your installation was successful, your terminal will return the versions of Python and `pip` that you installed.  **Note**: If you have `pyenv` it will install a specific version of Python for you.
 
 2. Install `pipenv` by running `pip install pipenv`.
     - If you already have `pipenv` installed, ensure that the version is >=2023.9.8 to avoid compatibility issues.

Dockerfile

@@ -8,15 +8,14 @@ RUN apt-get update \
     python3-dev \
     python3-setuptools \
     python3-pip \
-    python3-pandas \
     && rm -rf /var/lib/apt/lists/*
 
 RUN pip3 install --upgrade pip
 
 WORKDIR /synapsePythonClient
 COPY . .
 
-RUN pip install --no-cache-dir .
+RUN pip install --no-cache-dir .[pandas]
 
 
 LABEL org.opencontainers.image.source='https://github.com/Sage-Bionetworks/synapsePythonClient'