Add Python 3.13 to CI, modernize type hints now that 3.10 is the minimum supported Python (#28)

* bump lightning dev sha, minor doc cleanup, set CI to use python 3.13

* modernize type hints for python 3.10+)

* automate test warnings cleanup process, enhance CI infra scripts with new options

* adjust docs reqs and external role definitions for updated sphinx version

* minor format fixes

* prune commented warns

Author: speediedan

.azure-pipelines/gpu-tests.yml

@@ -47,7 +47,7 @@ jobs:
     strategy:
       matrix:
         'PyTorch | latest':
-          image: "speediedan/finetuning-scheduler:py3.12-pt2.10.0-pl2.6-azpl-init"
+          image: "speediedan/finetuning-scheduler:py3.13-pt2.10.0-pl2.6-azpl-init"
           scope: ""
     # how long to run the job before automatically cancelling
     timeoutInMinutes: "100"

.github/ISSUE_TEMPLATE/bug_report.md

@@ -42,7 +42,7 @@ You can also fill out the list below manually.
 - Fine-Tuning Scheduler Version (e.g., 2.10.0):
 - Lightning Version (e.g., 2.6.0):
 - PyTorch Version (e.g., 2.10.0):
-- Python version (e.g., 3.12):
+- Python version (e.g., 3.13):
 - OS (e.g., Linux):
 - CUDA/cuDNN version:
 - GPU models and configuration:

.github/actions/install-ci-dependencies/action.yml

@@ -5,7 +5,7 @@ inputs:
   python_version:
     description: "Python version to use"
     required: false
-    default: "3.12"
+    default: "3.13"
   use_oldest:
     description: "Whether to use oldest compatible versions (for testing min version support)"
     required: false

.github/copilot-instructions.md

@@ -6,7 +6,7 @@
 
 **Key Technologies:**
 
-- Python 3.9+ (CI tests on 3.9 and 3.12)
+- Python 3.9+ (CI tests on 3.10 and 3.13)
 - PyTorch 2.6.0+ with PyTorch Lightning ecosystem
 - Core deps: pytorch-lightning (standalone) or lightning (unified package), transformers
 
@@ -281,7 +281,7 @@ src/fts_examples/             # Example experiments
 **File:** `.github/workflows/ci_test-full.yml`
 
 **Triggers:** Push/PR to main, changes to source/test files
-**Platforms:** Ubuntu 22.04, Windows 2022, macOS 14 (Python 3.10, 3.12)
+**Platforms:** Ubuntu 22.04, Windows 2022, macOS 14 (Python 3.10, 3.13)
 **Timeout:** 90 minutes
 
 **Matrix Strategy:**
@@ -342,42 +342,53 @@ tail -f `ls -rt /tmp/gen_fts_coverage_fts_* | tail -1`
 **Common coverage commands:**
 
 ```bash
+# Note: Both --repo-home and --repo_home work (backward compatible)
+
 # Generate coverage with rebuild (fts_latest with stable PyTorch)
 ~/repos/finetuning-scheduler/scripts/manage_standalone_processes.sh --use-nohup \
   ~/repos/finetuning-scheduler/scripts/gen_fts_coverage.sh \
-  --repo_home=${HOME}/repos/finetuning-scheduler \
-  --target_env_name=fts_latest \
+  --repo-home=${HOME}/repos/finetuning-scheduler \
+  --target-env-name=fts_latest \
   --venv-dir=/mnt/cache/${USER}/.venvs
 
 # Generate coverage without rebuild
 ~/repos/finetuning-scheduler/scripts/manage_standalone_processes.sh --use-nohup \
   ~/repos/finetuning-scheduler/scripts/gen_fts_coverage.sh \
-  --repo_home=${HOME}/repos/finetuning-scheduler \
-  --target_env_name=fts_latest \
+  --repo-home=${HOME}/repos/finetuning-scheduler \
+  --target-env-name=fts_latest \
   --venv-dir=/mnt/cache/${USER}/.venvs \
-  --no_rebuild_base
+  --no-rebuild-base
 
 # Include experimental patch tests
 ~/repos/finetuning-scheduler/scripts/manage_standalone_processes.sh --use-nohup \
   ~/repos/finetuning-scheduler/scripts/gen_fts_coverage.sh \
-  --repo_home=${HOME}/repos/finetuning-scheduler \
-  --target_env_name=fts_latest \
+  --repo-home=${HOME}/repos/finetuning-scheduler \
+  --target-env-name=fts_latest \
+  --venv-dir=/mnt/cache/${USER}/.venvs \
+  --include-experimental
+
+# Run all example tests (comprehensive validation)
+~/repos/finetuning-scheduler/scripts/manage_standalone_processes.sh --use-nohup \
+  ~/repos/finetuning-scheduler/scripts/gen_fts_coverage.sh \
+  --repo-home=${HOME}/repos/finetuning-scheduler \
+  --target-env-name=fts_latest \
   --venv-dir=/mnt/cache/${USER}/.venvs \
-  --include_experimental
+  --no-rebuild-base \
+  --run-all-and-examples
 
 # Generate coverage with oldest dependencies (Python 3.10, mirrors CI oldest matrix)
 ~/repos/finetuning-scheduler/scripts/manage_standalone_processes.sh --use-nohup \
   ~/repos/finetuning-scheduler/scripts/gen_fts_coverage.sh \
-  --repo_home=${HOME}/repos/finetuning-scheduler \
-  --target_env_name=fts_oldest \
+  --repo-home=${HOME}/repos/finetuning-scheduler \
+  --target-env-name=fts_oldest \
   --venv-dir=/mnt/cache/${USER}/.venvs \
   --oldest
 
 # Generate coverage with oldest deps, skip special tests (faster CI-like run)
 ~/repos/finetuning-scheduler/scripts/manage_standalone_processes.sh --use-nohup \
   ~/repos/finetuning-scheduler/scripts/gen_fts_coverage.sh \
-  --repo_home=${HOME}/repos/finetuning-scheduler \
-  --target_env_name=fts_oldest \
+  --repo-home=${HOME}/repos/finetuning-scheduler \
+  --target-env-name=fts_oldest \
   --venv-dir=/mnt/cache/${USER}/.venvs \
   --oldest \
   --no-special
@@ -387,6 +398,8 @@ tail -f `ls -rt /tmp/gen_fts_coverage_fts_* | tail -1`
 
 - `--oldest`: Uses Python 3.10 and `requirements/ci/requirements-oldest.txt` (mirrors CI oldest matrix)
 - `--no-special`: Skips `special_tests.sh` standalone and experimental patch tests (faster iteration)
+- `--run-all-and-examples`: Runs all example tests (both non-standalone and standalone marked)
+- `--allow-failures`: Continues test execution after failures (useful for validation workflows)
 - `--venv-dir`: Base directory for venvs (recommended: `/mnt/cache/${USER}/.venvs` for hardlink performance)
 
 ## Special Dependencies and Known Issues

.github/workflows/ci_test-full.yml

@@ -44,17 +44,17 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-22.04, windows-2022, macOS-14]
-        python-version: ["3.10", "3.12"]  # minimum, maximum
+        python-version: ["3.10", "3.13"]  # minimum, maximum
         # tests will include oldest and newest tested patch versions of pytorch
         requires: ["oldest", "latest"]
         release: ["latest"]
         exclude:  # note that occasionally, the oldest PyTorch version does not support the latest python version
-          - {os: ubuntu-22.04, python-version: "3.12", requires: "oldest"}
-          - {os: windows-2022, python-version: "3.12", requires: "oldest"}
-          - {os: macOS-14, python-version: "3.12", requires: "oldest"}
+          - {os: ubuntu-22.04, python-version: "3.13", requires: "oldest"}
+          - {os: windows-2022, python-version: "3.13", requires: "oldest"}
+          - {os: macOS-14, python-version: "3.13", requires: "oldest"}
         # include:
         #   # adding when using a release candidate
-        #   # - {os: ubuntu-22.04, python-version: "3.12", requires: "latest", release: "pre"}
+        #   # - {os: ubuntu-22.04, python-version: "3.13", requires: "latest", release: "pre"}
 
     timeout-minutes: 90
     env:

.github/workflows/code-checks.yml

@@ -53,7 +53,7 @@ jobs:
       - name: Install CI Dependencies
         uses: ./.github/actions/install-ci-dependencies
         with:
-          python_version: "3.12"
+          python_version: "3.13"
           use_commit_pin: "true"
           show_pip_list: "true"
 

.github/workflows/copilot-setup-steps.yml

@@ -23,7 +23,7 @@ jobs:
       - name: Install CI dependencies
         uses: ./.github/actions/install-ci-dependencies
         with:
-          python_version: '3.12'
+          python_version: '3.13'
           show_pip_list: 'true'
 
       - name: Install pre-commit

.github/workflows/release-docker.yml

@@ -30,7 +30,7 @@ jobs:
       fail-fast: false
       matrix:
         # initially building only the latest supported configuration
-        python_version: ["3.12"]
+        python_version: ["3.13"]
         pytorch_version: ["2.10.0"]
         cust_base: ["cu12.8.1-"]
         pl_version: ["2.6"]

.github/workflows/release-pypi.yml

@@ -28,7 +28,7 @@ jobs:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
       with:
-        python-version: '3.12'
+        python-version: '3.13'
 
     - name: Install dependencies
       run: >-

.readthedocs.yml

@@ -39,7 +39,7 @@ formats:
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.12"
+    python: "3.13"
   apt_packages:
     - texlive-latex-extra
     - dvipng