Squashed commit of the following:

commit 5d8457c4495491490ed220564e1002284f0a9215 Author: David Meyer <[email protected]> Date: Fri Feb 9 12:09:00 2024 -0500 Merge pull request #112 from dihm/setuptools_scm_fix Ensure setuptools_scm always uses `release-branch-semver`. commit 03c7e19c7afa35fc088212907f5fbb714007162a Author: David Meyer <[email protected]> Date: Fri Feb 9 12:05:59 2024 -0500 Merge pull request #113 from dihm/update_workflow Update workflow pins to upgrade node.js to 20. commit 0ab9b30678e4bc5582c791e67659618b30ad6211 Author: David Meyer <[email protected]> Date: Thu Jan 18 20:59:22 2024 -0500 Merge pull request #111 from dihm/rtd_build Modernize RTD build commit 00ffd6c498178e11a7c8fa275632543126313db9 Author: David Meyer <[email protected]> Date: Thu Oct 12 16:17:57 2023 -0400 Merge pull request #110 from dihm/get_shot_globals_deprecation Get shot globals deprecation
labscript-suite · Feb 9, 2024 · 34e1442 · 34e1442
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diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -64,7 +64,7 @@ jobs:
     if: github.repository == 'labscript-suite/runmanager' && (github.event_name != 'create' || github.event.ref_type != 'branch')
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -73,7 +73,7 @@ jobs:
         run: git tag -d $(git tag --points-at HEAD)
 
       - name: Install Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
           architecture: ${{ matrix.arch }}
@@ -93,7 +93,7 @@ jobs:
 
       - name: Upload Artifact
         if: strategy.job-index == 0 || (env.PURE == 'false' && runner.os != 'Linux')
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: dist
           path: ./dist
@@ -111,7 +111,7 @@ jobs:
 
       - name: Install Miniconda
         if: matrix.conda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python }}
@@ -140,7 +140,7 @@ jobs:
 
       - name: Upload Artifact
         if: matrix.conda
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: conda_packages
           path: ./conda_packages
@@ -153,7 +153,7 @@ jobs:
     steps:
       - name: Checkout
         if: env.PURE == 'false'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -170,7 +170,7 @@ jobs:
 
       - name: Upload Artifact
         if: env.PURE == 'false'
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: dist
           path: dist/*manylinux*.whl
@@ -182,13 +182,13 @@ jobs:
     steps:
 
       - name: Download Artifact
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: dist
           path: ./dist
 
       - name: Download Artifact
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: conda_packages
           path: ./conda_packages
@@ -226,7 +226,7 @@ jobs:
           password: ${{ secrets.pypi }}
 
       - name: Install Miniconda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
 

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -13,8 +13,6 @@
 import copy
 import os
 from pathlib import Path
-from m2r import MdInclude
-from recommonmark.transform import AutoStructify
 from jinja2 import FileSystemLoader, Environment
 try:
     import importlib.metadata as importlib_metadata
@@ -51,7 +49,7 @@
     "sphinx.ext.todo",
     "sphinx.ext.viewcode",
     "sphinx_rtd_theme",
-    "recommonmark",
+    "myst_parser",
 ]
 
 autodoc_typehints = 'description'
@@ -108,6 +106,7 @@ def set_process_name(self,*args,**kwargs):
 
 # Prefix each autosectionlabel with the name of the document it is in and a colon
 autosectionlabel_prefix_document = True
+myst_heading_anchors = 2
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -246,23 +245,8 @@ def set_process_name(self,*args,**kwargs):
 # Customize the html_theme
 html_theme_options = {'navigation_depth': 3}
 
-# Use m2r only for mdinclude and recommonmark for everything else
-# https://github.com/readthedocs/recommonmark/issues/191#issuecomment-622369992
 def setup(app):
-    config = {
-        # 'url_resolver': lambda url: github_doc_root + url,
-        'auto_toc_tree_section': 'Contents',
-        'enable_eval_rst': True,
-    }
-    app.add_config_value('recommonmark_config', config, True)
-    app.add_transform(AutoStructify)
-
-    # from m2r to make `mdinclude` work
-    app.add_config_value('no_underscore_emphasis', False, 'env')
-    app.add_config_value('m2r_parse_relative_links', False, 'env')
-    app.add_config_value('m2r_anonymous_references', False, 'env')
-    app.add_config_value('m2r_disable_inline_math', False, 'env')
-    app.add_directive('mdinclude', MdInclude)
+
     app.add_css_file('custom.css')
 
     # generate the components.rst file dynamically so it points to stable/latest

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,3 +1,5 @@
 [build-system]
-requires = ["setuptools", "wheel", "setuptools_scm"]
+requires = ["setuptools>=64", "wheel", "setuptools_scm>=8"]
 build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
diff --git a/readthedocs.yaml b/readthedocs.yaml
@@ -4,6 +4,12 @@
 # Required
 version: 2
 
+# Set build environment options
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   builder: dirhtml
@@ -15,13 +21,11 @@ formats:
   - pdf
   - epub
 
-# Optionally set the version of Python and requirements required to build your docs
+# Optionally set the requirements required to build your docs
 python:
-   version: 3.7
    install:
       - method: pip
         path: .
         extra_requirements:
             - docs
-   system_packages: true
 
diff --git a/runmanager/__init__.py b/runmanager/__init__.py
@@ -25,13 +25,15 @@
 import json
 import tokenize
 import io
+import warnings
 
 import labscript_utils.h5_lock
 import h5py
 import numpy as np
 
 from labscript_utils.ls_zprocess import ProcessTree, zmq_push_multipart
 from labscript_utils.labconfig import LabConfig
+import labscript_utils.shot_utils
 process_tree = ProcessTree.instance()
 
 from .__version__ import __version__
@@ -915,24 +917,16 @@ def compile_labscript_with_globals_files_async(labscript_file, globals_files, ou
 def get_shot_globals(filepath):
     """Returns the evaluated globals for a shot, for use by labscript or lyse.
     Simple dictionary access as in dict(h5py.File(filepath).attrs) would be fine
-    except we want to apply some hacks, so it's best to do that in one place."""
-    params = {}
-    with h5py.File(filepath, 'r') as f:
-        for name, value in f['globals'].attrs.items():
-            # Convert numpy bools to normal bools:
-            if isinstance(value, np.bool_):
-                value = bool(value)
-            # Convert null HDF references to None:
-            if isinstance(value, h5py.Reference) and not value:
-                value = None
-            # Convert numpy strings to Python ones.
-            # DEPRECATED, for backward compat with old files.
-            if isinstance(value, np.str_):
-                value = str(value)
-            if isinstance(value, bytes):
-                value = value.decode()
-            params[name] = value
-    return params
+    except we want to apply some hacks, so it's best to do that in one place.
+    
+    Deprecated: use identical function `labscript_utils.shot_utils.get_shot_globals`
+    """
+
+    warnings.warn(
+        FutureWarning("get_shot_globals has moved to labscript_utils.shot_utils. "
+                      "Please update your code to import it from there."))
+
+    return labscript_utils.shot_utils.get_shot_globals(filepath)
 
 
 def dict_diff(dict1, dict2):

diff --git a/runmanager/__version__.py b/runmanager/__version__.py
@@ -6,7 +6,7 @@
     import importlib_metadata
 
 VERSION_SCHEME = {
-    "version_scheme": os.getenv("SCM_VERSION_SCHEME", "guess-next-dev"),
+    "version_scheme": os.getenv("SCM_VERSION_SCHEME", "release-branch-semver"),
     "local_scheme": os.getenv("SCM_LOCAL_SCHEME", "node-and-date"),
 }
 

diff --git a/setup.cfg b/setup.cfg
@@ -31,7 +31,7 @@ install_requires =
   desktop-app>=0.1.2
   importlib_metadata
   labscript>=3.0.0
-  labscript_utils>=3.0.0
+  labscript_utils>=3.3.0
   pandas>=0.13
   qtutils>=2.2.2
   matplotlib
@@ -46,8 +46,6 @@ gui_scripts =
 pyqt = PyQt5
 docs = 
   PyQt5
-  Sphinx==4.4.0
-  sphinx-rtd-theme==0.5.2
-  recommonmark==0.6.0
-  m2r==0.2.1
-  mistune<2.0.0
+  Sphinx==7.2.6
+  sphinx-rtd-theme==2.0.0
+  myst_parser==2.0.0
diff --git a/setup.py b/setup.py
@@ -2,7 +2,7 @@
 from setuptools import setup
 
 VERSION_SCHEME = {
-    "version_scheme": os.getenv("SCM_VERSION_SCHEME", "guess-next-dev"),
+    "version_scheme": os.getenv("SCM_VERSION_SCHEME", "release-branch-semver"),
     "local_scheme": os.getenv("SCM_LOCAL_SCHEME", "node-and-date"),
 }