Merge branch 'synpy-1636-move-to-electron' into synpy-1653-sign-mac-os-standalone

Author: BryanFauble

.github/scripts/delete_evaluations.py

@@ -4,7 +4,7 @@
 from synapseclient import Evaluation, Synapse
 
 syn = Synapse()
-syn.login()
+syn.login(profile=None)
 
 # Maximum number of concurrent deletion operations
 MAX_CONCURRENT_DELETIONS = 5

.github/scripts/delete_projects.py

@@ -4,7 +4,7 @@
 from synapseclient import Synapse
 
 syn = Synapse()
-syn.login()
+syn.login(profile=None)
 
 # Maximum number of concurrent deletion operations
 MAX_CONCURRENT_DELETIONS = 5

.github/scripts/delete_teams.py

@@ -4,7 +4,7 @@
 from synapseclient import Synapse
 
 syn = Synapse()
-syn.login()
+syn.login(profile=None)
 
 # Maximum number of concurrent team deletions
 MAX_CONCURRENT_DELETIONS = 5

.github/scripts/empty_trash.py

@@ -4,7 +4,7 @@
 from synapseclient import Synapse
 
 syn = Synapse()
-syn.login()
+syn.login(profile=None)
 
 # Maximum number of concurrent deletion operations
 MAX_CONCURRENT_DELETIONS = 5

.github/workflows/build.yml

@@ -63,7 +63,7 @@ jobs:
 
         # 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', '3.13']
+        python: ['3.10', '3.11', '3.12', '3.13', '3.14']
 
     runs-on: ${{ matrix.os }}
 
@@ -92,7 +92,7 @@ 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') }}-v28
+          key: ${{ runner.os }}-${{ matrix.python }}-build-${{ env.cache-name }}-${{ hashFiles('setup.py') }}-v29
 
       - name: Install py-dependencies
         if: steps.cache-dependencies.outputs.cache-hit != 'true'
@@ -117,7 +117,7 @@ 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('["3.13"]'), matrix.python) }}
+        if: ${{ contains(fromJSON('["3.10"]'), matrix.python) || contains(fromJSON('["3.14"]'), matrix.python) }}
         # perform secret check & put boolean result as an output
         shell: bash
         run: |
@@ -134,7 +134,7 @@ jobs:
           fi
 
       - name: Download Failed Tests from Previous Attempt
-        if: ${{ github.run_attempt > 1 && (contains(fromJSON('["3.9"]'), matrix.python) || contains(fromJSON('["3.13"]'), matrix.python)) && steps.secret-check.outputs.secrets_available == 'true'}}
+        if: ${{ github.run_attempt > 1 && (contains(fromJSON('["3.10"]'), matrix.python) || contains(fromJSON('["3.14"]'), matrix.python)) && steps.secret-check.outputs.secrets_available == 'true'}}
         uses: actions/download-artifact@v4
         with:
           name: failed-tests-${{ matrix.os }}-${{ matrix.python }}
@@ -150,25 +150,25 @@ jobs:
         shell: bash
 
         # keep versions consistent with the first and last from the strategy matrix
-        if: ${{ (contains(fromJSON('["3.9"]'), matrix.python) || contains(fromJSON('["3.13"]'), matrix.python)) && steps.secret-check.outputs.secrets_available == 'true'}}
+        if: ${{ (contains(fromJSON('["3.10"]'), matrix.python) || contains(fromJSON('["3.14"]'), matrix.python)) && steps.secret-check.outputs.secrets_available == 'true'}}
         run: |
           # Set SYNAPSE_PROFILE based on OS and Python version
           if [ "${{ startsWith(matrix.os, 'ubuntu') }}" == "true" ]; then
-            if [ "${{ matrix.python }}" == "3.9" ]; then
+            if [ "${{ matrix.python }}" == "3.10" ]; then
               export SYNAPSE_PROFILE="TestUbuntuMinimumPython"
-            elif [ "${{ matrix.python }}" == "3.13" ]; then
+            elif [ "${{ matrix.python }}" == "3.14" ]; then
               export SYNAPSE_PROFILE="TestUbuntuMaximumPython"
             fi
           elif [ "${{ startsWith(matrix.os, 'windows') }}" == "true" ]; then
-            if [ "${{ matrix.python }}" == "3.9" ]; then
+            if [ "${{ matrix.python }}" == "3.10" ]; then
               export SYNAPSE_PROFILE="TestWindowsMinimumPython"
-            elif [ "${{ matrix.python }}" == "3.13" ]; then
+            elif [ "${{ matrix.python }}" == "3.14" ]; then
               export SYNAPSE_PROFILE="TestWindowsMaximumPython"
             fi
           elif [ "${{ startsWith(matrix.os, 'macos') }}" == "true" ]; then
-            if [ "${{ matrix.python }}" == "3.9" ]; then
+            if [ "${{ matrix.python }}" == "3.10" ]; then
               export SYNAPSE_PROFILE="TestMacosMinimumPython"
-            elif [ "${{ matrix.python }}" == "3.13" ]; then
+            elif [ "${{ matrix.python }}" == "3.14" ]; then
               export SYNAPSE_PROFILE="TestMacosMaximumPython"
             fi
           fi
@@ -210,16 +210,6 @@ jobs:
           # Setup ignore patterns based on Python version
           IGNORE_FLAGS="--ignore=tests/integration/synapseclient/test_command_line_client.py"
 
-          if [ "${{ matrix.python }}" == "3.9" ]; then
-            # For min Python version, ignore async tests
-            IGNORE_FLAGS="$IGNORE_FLAGS --ignore=tests/integration/synapseclient/models/async/"
-            echo "Running integration tests for Min Python version (3.9) - ignoring async tests"
-          elif [ "${{ matrix.python }}" == "3.13" ]; then
-            # For max Python version, ignore synchronous tests
-            IGNORE_FLAGS="$IGNORE_FLAGS --ignore=tests/integration/synapseclient/models/synchronous/"
-            echo "Running integration tests for Max Python version (3.13) - ignoring synchronous tests"
-          fi
-
           # Check if we should run only failed tests from previous attempt
           if [[ -f failed_tests.txt && -s failed_tests.txt ]]; then
             echo "::notice::Retry attempt ${{ github.run_attempt }} detected - running only previously failed tests"
@@ -370,7 +360,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.10
 
       - name: set-release-env
         shell: bash
@@ -680,7 +670,7 @@ jobs:
         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', '3.13']
+        python: ['3.10', '3.11', '3.12', '3.13', '3.14']
 
     runs-on: ${{ matrix.os }}
 

.github/workflows/test-cleanup.yml

@@ -13,6 +13,17 @@ jobs:
     permissions:
       contents: read
 
+    strategy:
+      matrix:
+        synapse_profile:
+          - "TestUbuntuMinimumPython"
+          - "TestUbuntuMaximumPython"
+          - "TestWindowsMinimumPython"
+          - "TestWindowsMaximumPython"
+          - "TestMacosMinimumPython"
+          - "TestMacosMaximumPython"
+          - "" # Empty string for default profile (no SYNAPSE_PROFILE set)
+
     steps:
     - name: Checkout repository
       uses: actions/checkout@v4
@@ -67,17 +78,33 @@ jobs:
         mv test.synapseConfig ~/.synapseConfig
 
     - name: Run evaluation deletion script
+      shell: bash
       run: |
+        if [ -n "${{ matrix.synapse_profile }}" ]; then
+          export SYNAPSE_PROFILE="${{ matrix.synapse_profile }}"
+        fi
         python .github/scripts/delete_evaluations.py
 
     - name: Run project deletion script
+      shell: bash
       run: |
+        if [ -n "${{ matrix.synapse_profile }}" ]; then
+          export SYNAPSE_PROFILE="${{ matrix.synapse_profile }}"
+        fi
         python .github/scripts/delete_projects.py
 
     - name: Run team deletion script
+      shell: bash
       run: |
+        if [ -n "${{ matrix.synapse_profile }}" ]; then
+          export SYNAPSE_PROFILE="${{ matrix.synapse_profile }}"
+        fi
         python .github/scripts/delete_teams.py
 
     - name: Run empty trash script
+      shell: bash
       run: |
+        if [ -n "${{ matrix.synapse_profile }}" ]; then
+          export SYNAPSE_PROFILE="${{ matrix.synapse_profile }}"
+        fi
         python .github/scripts/empty_trash.py

.gitignore

@@ -6,6 +6,7 @@ virtualenvs
 examples_temp
 .DS_Store
 deploy.sh
+.venv/
 
 junk/
 nose.cfg
@@ -33,6 +34,7 @@ coverage.xml
 .ipynb_checkpoints
 *.ipynb
 .env
+test.synapseConfig
 *.spec
 
 synapse-electron/node_modules

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 <=3.13. 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.
+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 >=3.10 and <=3.14. 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.
@@ -223,6 +223,64 @@ When integration tests are ran in the Github CI/CD pipeline it will upload the t
 #### Integration testing for external collaborators
 As an external collaborator you will not have access to a development account and environment to run the integration tests against. Either request that a Sage Bionetworks staff member run your integration tests via a pull request, or, contact us via the [Service Desk](https://sagebionetworks.jira.com/servicedesk/customer/portal/9) to requisition a development account for integration testing only.
 
+### Managing Python version changes
+
+When adding support for a new Python version or dropping support for an old version, several files across the codebase and CI/CD pipelines must be updated to ensure consistency and proper testing coverage.
+
+#### Adding a new Python version
+
+When adding support for a new Python version (e.g., adding Python 3.15), update the following:
+
+**Code configuration files:**
+1. **`setup.cfg`**:
+   - Add the new version to the `classifiers` list under `[metadata]` (e.g., `Programming Language :: Python :: 3.15`)
+   - Update the `python_requires` constraint under `[options]` to include the new version (e.g., `>=3.10, <3.16`)
+
+2. **`pyproject.toml`**:
+   - Update the `target-version` list in the `[tool.black]` section to include the new version if needed
+
+3. **`Dockerfile`**:
+   - Update the base image to use the new Python version (e.g., `FROM python:3.15-slim`)
+
+**CI/CD configuration files:**
+1. **`.github/workflows/build.yml`**:
+   - Add the new version to the `python` matrix under the `test` job strategy
+   - Ensure the new version is included in integration test runs (typically the latest version should be tested)
+   - Update any Python version comments or documentation within the workflow
+
+**Testing:**
+- Run the full test suite (both unit and integration tests) on the new Python version locally before submitting a PR
+- Verify that all CI/CD pipelines pass with the new version included
+
+#### Dropping an old Python version
+
+When dropping support for an old Python version (e.g., removing Python 3.10), update the following:
+
+**Code configuration files:**
+1. **`setup.cfg`**:
+   - Remove the old version from the `classifiers` list under `[metadata]`
+   - Update the `python_requires` constraint under `[options]` to reflect the new minimum version (e.g., `>=3.11, <3.15`)
+
+2. **`pyproject.toml`**:
+   - Update the `target-version` list in the `[tool.black]` section to remove the old version
+
+3. **`Dockerfile`**:
+   - Ensure the base image uses a supported Python version
+
+**CI/CD configuration files:**
+1. **`.github/workflows/build.yml`**:
+   - Remove the old version from the `python` matrix under the `test` job strategy
+   - Update the cache key version (e.g., increment `v28` to `v29`) to invalidate old caches
+
+**Documentation:**
+- Update the README.md and any getting started documentation to reflect the new supported Python version range
+- Update CONTRIBUTING.md (this file) if it mentions specific Python versions in examples
+
+**Important considerations:**
+- Python version changes should be coordinated with a release and clearly communicated in release notes
+- Breaking compatibility with a Python version is a significant change and should typically coincide with a major or minor version bump
+- Always test thoroughly on the minimum and maximum supported Python versions before release
+
 ### Asynchronous methods
 [Asyncio](https://docs.python.org/3/library/asyncio.html) is the future of the Synapse
 Python Client. As such, the expectation is that all future methods that rely on async

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.9-slim
+FROM python:3.14-slim
 RUN echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selections
 
 RUN apt-get update \

Pipfile

@@ -10,4 +10,4 @@ synapseclient = {file = ".", path = "."}
 python_version = "3.12.6"
 
 [dev-packages]
-synapseclient = {file = ".", editable = true, path = ".", extras = ["dev", "tests", "pandas", "pysftp", "boto3", "docs"]}
+synapseclient = {file = ".", editable = true, path = ".", extras = ["dev", "tests", "pandas", "pysftp", "boto3", "docs", "curator"]}