sciris 3.2.5__tar.gz → 3.2.8__tar.gz

{sciris-3.2.5 → sciris-3.2.8}/.github/workflows/schedule_tests.yaml

@@ -2,7 +2,7 @@ name: Sciris cron tests
 on:
   workflow_dispatch:
   schedule:
-    - cron: "0 0 * * 0" # Run every Sunday at midnight
+    - cron: "0 0 * * *" # Run every day at midnight
 
 jobs:
   ci-tests:

sciris-3.2.8/.pylintrc

@@ -0,0 +1,116 @@
+[BASIC]
+
+# Regular expression matching correct argument names. Overrides argument-
+# naming-style. If left empty, argument names will be checked with the set
+# naming style.
+argument-rgx=[a-z_][a-z0-9_]{0,15}$ # Sciris
+variable-rgx=[a-z_][a-z0-9_]{0,15}$ # Sciris
+attr-rgx=[a-z_][a-z0-9_]{0,15}$ # Sciris
+class-attribute-rgx=[a-z_][a-z0-9_]{0,15}$ # Sciris
+function-rgx=[a-z_][a-z0-9_]{0,15}$ # Sciris
+method-rgx=[a-z_][a-z0-9_]{0,15}$ # Sciris
+class-rgx=[a-zA-Z_][a-zA-Z0-9_]{0,15}$ # Sciris
+
+# Good variable names which should always be accepted, separated by a comma.
+good-names=E # Sciris
+
+
+[DESIGN]
+
+# Maximum number of arguments for function / method.
+max-args=20 # Sciris
+
+# Maximum number of attributes for a class (see R0902).
+max-attributes=20 # Sciris
+
+# Maximum number of boolean expressions in an if statement (see R0916).
+max-bool-expr=5
+
+# Maximum number of branch for function / method body.
+max-branches=15 # Sciris
+
+# Maximum number of locals for function / method body.
+max-locals=20 # Sciris
+
+# Maximum number of parents for a class (see R0901).
+max-parents=7
+
+# Maximum number of public methods for a class (see R0904).
+max-public-methods=20
+
+# Maximum number of return / yield for function / method body.
+max-returns=5 # Sciris
+
+# Maximum number of statements in function / method body.
+max-statements=200 # Sciris
+
+# Minimum number of public methods for a class (see R0903).
+min-public-methods=2
+
+
+[FORMAT]
+
+# Maximum number of characters on a single line.
+max-line-length=200 # Sciris
+
+# Maximum number of lines in a module.
+max-module-lines=2000 # Sciris
+
+# Allow the body of an if to be on the same line as the test if there is no
+# else.
+single-line-if-stmt=yes # Sciris
+
+
+[IMPORTS]
+
+# Allow wildcard imports from modules that define __all__.
+allow-wildcard-with-all=yes # Sciris
+
+
+[MESSAGES CONTROL]
+
+# Disable the message, report, category or checker with the given id(s). You
+# can either give multiple identifiers separated by comma (,) or put this
+# option multiple times (only on the command line, not in the configuration
+# file where it should appear only once). You can also use "--disable=all" to
+# disable everything first and then re-enable specific checks. For example, if
+# you want to run only the similarities checker, you can use "--disable=all
+# --enable=similarities". If you want to run only the classes checker, but have
+# no Warning level messages displayed, use "--disable=all --enable=classes
+# --disable=W".
+disable=raw-checker-failed,
+        bad-inline-option,
+        locally-disabled,
+        file-ignored,
+        suppressed-message,
+        useless-suppression,
+        deprecated-pragma,
+        use-symbolic-message-instead,
+        C0103, # Sciris: allow lowercase constants
+        C0321, # Sciris: multiple statements on a line
+        C0325, # Sciris: allow parentheses in if
+        C0411, # Sciris: allow different import order
+        C0412, # Sciris: allow ungrouped imports
+        C0413, # Sciris: allow imports not at the top
+        E1101, # Sciris: don't check class membership (dynamic classes)
+        R1705, # Sciris: allow else-return
+        R1711, # Sciris: empty return
+        R1720, # Sciris: allow else after raise
+        R1735, # Sciris: dict literal
+        W0702, # Sciris: allow bare except
+        W0718 # Sciris: allow general exception
+
+# Enable the message, report, category or checker with the given id(s). You can
+# either give multiple identifier separated by comma (,) or put this option
+# multiple time (only on the command line, not in the configuration file where
+# it should appear only once). See also the "--disable" option for examples.
+enable=c-extension-no-member
+
+
+[MISCELLANEOUS]
+
+# List of note tags to take in consideration, separated by a comma.
+notes=FIXME,
+      XXX,
+      TODO,
+      TEMP # Sciris

{sciris-3.2.5 → sciris-3.2.8}/CHANGELOG.rst

@@ -7,9 +7,32 @@ All major updates to Sciris are documented here.
 
 By import convention, components of the Sciris library are listed beginning with ``sc.``, e.g. ``sc.odict()``.
 
+Version 3.2.8 (2026-02-28)
+--------------------------
+#. Changed resolution order in :class:`sc.objdict() <sc_odict.objdict>` so that dunder attributes (e.g. ``__await__``) are never accidentally set as dict keys. Attempting to set an existing attribute as a key now raises ``KeyError`` instead of ``ValueError``.
+#. Fixed a bug in :class:`sc.profile() <sc_profiling.profile>` that prevented profiling information from being printed for certain combinations of filenames.
+
+Version 3.2.7 (2026-02-18)
+--------------------------
+#. Refactored :class:`sc.asd() <sc_asd.asd>` to be more robust to different parameter inputs and different objective function return values.
+
+Version 3.2.6 (2026-02-12)
+--------------------------
+#. Added :class:`sc.argparse() <sc_odict.argparse>`, a simple argument parser based on ``sc.objdict``.
+#. :class:`sc.objdict() <sc_odict.objdict>` now has an ``update()`` method, as well as improved pickling support via ``__reduce__()`` and ``__setstate__()``.
+#. :func:`sc.sigfig() <sc_printing.sigfig>` now has a ``formats`` argument for customizing SI unit formatting, and uses ``'g'`` format when ``sigfigs=None``.
+#. :func:`sc.parallelize() <sc_parallel.parallelize>` now has improved exception handling, providing clearer error messages when tasks fail.
+#. :class:`sc.profile() <sc_profiling.profile>` now properly disables the profiler after running, and has improved function name parsing.
+
 Version 3.2.5 (2026-01-27)
 --------------------------
-#. Updated :func`sc.dataframe.replacedata()` <sc_dataframe.dataframe.replacedata> with support for Pandas 3.0
+#. Updated :func:`sc.dataframe.replacedata() <sc_dataframe.dataframe.replacedata>` with support for Pandas 3.0.
+#. :class:`sc.timer() <sc_datetime.timer>` now has a ``string`` attribute for returning formatted time strings.
+#. :func:`sc.parallelize() <sc_parallel.parallelize>` now has ``capture`` and ``lbkwargs`` arguments for capturing task output and passing load balancer options.
+#. :func:`sc.loadbalancer() <sc_parallel.loadbalancer>` has been moved from ``sc_profiling`` to ``sc_parallel`` for better organization.
+#. Fixed a bug in :func:`sc.SIticks() <sc_plotting.SIticks>` that caused incorrect tick formatting.
+#. :class:`sc.profile() <sc_profiling.profile>` now handles cases when another profiler is already running.
+#. :func:`sc.options() <sc_settings.options>` now prevents accidental modification by raising an error when attempting to set invalid options.
 
 Version 3.2.4 (2025-07-12)
 --------------------------

{sciris-3.2.5 → sciris-3.2.8}/CLAUDE.md

@@ -6,7 +6,7 @@ This file provides guidance to Claude Code (claude.ai/code) when working with co
 
 **Citation**: Kerr CC, Sanz-Leon P, Abeysuriya RG, et al. Sciris: Simplifying scientific software in Python. *Journal of Open Source Software*. 2023;8(88):5076. doi:10.21105/joss.05076
 
-**Key Applications**: Used by Covasim (COVID-19 modeling), Optima HIV, Optima Nutrition, Atomica, and other scientific software tools adopted in 30+ countries.
+**Key Applications**: Used by Starsim (general-purpose disease modeling), Covasim, Optima HIV, Optima Nutrition, Atomica, and other scientific software tools adopted in 30+ countries.
 
 ## Quick Reference
 
@@ -32,28 +32,40 @@ This file provides guidance to Claude Code (claude.ai/code) when working with co
 ## Development Commands
 
 ### Testing
-- **Run all tests:** `cd tests && ./run_tests` (uses pytest with parallel execution)
+- **Install test requirements first:** `pip install -r tests/requirements.txt` (adds pytest, pytest-cov, pytest-xdist)
+- **Run all tests:** `cd tests && ./run_tests` (uses pytest with parallel execution via pytest-xdist)
 - **Run specific test:** `cd tests && pytest test_<module>.py -v`
 - **Check test coverage:** `cd tests && ./check_coverage` (generates HTML report at tests/htmlcov/index.html)
+- **Test downstream packages:** `cd tests/regression && ./run_downstream` (tests covasim, hpvsim, fpsim, atomica)
 - **Environment:** Tests run with `SCIRIS_BACKEND=agg` to prevent matplotlib windows
 
 ### Code Quality
-- **Linting:** No formal linter configured (project follows internal style guide)
-- **Type checking:** Not enforced (Sciris prioritizes flexibility over strict typing)
+- **Linting:** Uses pylint with custom .pylintrc; `cd tests && ./check_style` (generates text report at tests/pylint_report.txt)
+- **Type checking:** Do not use type hints (Sciris prioritizes flexibility over strict typing)
 - **Pre-commit hooks:** Not configured
-- **Style guide:** Follow existing code patterns and Python conventions
+- **Style guide:** See https://github.com/starsimhub/styleguide/blob/main/README.rst
 
 ### Documentation
 - **Build docs:** `cd docs && ./build_docs` (builds Sphinx documentation)
 - **Build docs without notebooks:** `cd docs && ./build_docs never`
 - **Debug mode (serial):** `cd docs && ./build_docs debug`
-- **Output:** Documentation built to docs/_build/html/index.html
+- **Output:** Documentation built to `docs/_build/html/index.html`
 
 ### Development Setup
 - **Install package:** `pip install -e .` (editable install from pyproject.toml)
 - **Test requirements:** `pip install -r tests/requirements.txt`
 - **Python version:** Requires Python >=3.9
 
+### Git Workflow
+- **Main branch:** `main` (use this as base for PRs)
+- **Feature branches:** Create descriptive branch names (e.g., `update-profiler`)
+
+### Continuous Integration
+- **Main test workflow:** `.github/workflows/test_sciris.yaml` (runs on push/PR)
+- **Scheduled tests:** `.github/workflows/schedule_tests.yaml` (periodic testing)
+- **Downstream tests:** `.github/workflows/test_downstream.yaml` (tests dependent packages)
+- **Release workflow:** `.github/workflows/pypi_release.yaml` (automated PyPI publishing)
+
 ## Architecture Overview
 
 Sciris is a scientific Python utilities library with a modular design organized around functional domains. Published in the Journal of Open Source Software (JOSS), Sciris aims to streamline the development of scientific software by making it easier to perform common tasks through "simplifying interfaces" that reduce boilerplate code and focus on scientific clarity.
@@ -223,10 +235,6 @@ Sciris functions accept multiple input types (lists, arrays, scalars) and handle
   - Default: System default
   - Example: `export SCIRIS_BACKEND=agg` (for headless environments)
 
-- **`SCIRIS_LAZY`**: Enable lazy loading for optional dependencies
-  - Default: False
-  - Example: `export SCIRIS_LAZY=1`
-
 ### Usage in Code
 ```python
 import os
@@ -261,14 +269,6 @@ When developing Sciris itself, modules use:
 import sciris as sc  # Even internal modules use this pattern
 ```
 
-### Specific Module Access
-For performance-critical code or when you need only specific functionality:
-```python
-import sciris as sc
-# Then use: sc.odict(), sc.save(), etc.
-# This is preferred over direct module imports
-```
-
 ## Common Development Patterns
 
 ### Adding New Functions
@@ -309,9 +309,8 @@ All I/O functions handle both file paths and file objects, with automatic compre
 - **Memory-constrained environments**: Sciris's convenience features use additional memory
 
 ### Common Pitfalls
-- **`die` parameter confusion**: Remember `die=False` = soft warnings, `die=True` = strict exceptions
+- **`die` parameter**: Remember `die=False` = soft warnings, `die=True` = strict exceptions
 - **Import order**: Always use `import sciris as sc` rather than individual module imports
-- **Thread limits**: Respect `SCIRIS_NUM_THREADS` environment variable in parallel code
 - **Type assumptions**: Don't assume specific return types - Sciris prioritizes flexibility over strict typing
 
 ### Migration Strategies
@@ -365,15 +364,4 @@ print(f"Thread limit: {os.environ.get('SCIRIS_NUM_THREADS', 'auto')}")
 
 # Monitor memory usage during operations
 sc.checkmem()  # Shows current memory usage
-```
-
-### Common Debug Patterns
-```python
-# Type checking and conversion
-data = sc.promotetoarray(data, verbose=True)  # Shows conversion details
-sc.checktype(data, 'arraylike', die=False)    # Non-fatal type check
-
-# Container inspection
-od = sc.odict(a=1, b=2, c=3)
-print(od.disp())  # Detailed container info
 ```

{sciris-3.2.5/sciris.egg-info → sciris-3.2.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sciris
-Version: 3.2.5
+Version: 3.2.8
 Summary: Fast, flexible tools to simplify scientific Python
 Author-email: Sciris Development Team <info@sciris.org>
 License-Expression: MIT

sciris-3.2.8/context7.json

@@ -0,0 +1,4 @@
+{
+  "url": "https://context7.com/sciris/sciris",
+  "public_key": "pk_RAjZiMtFTxRqXHnY6XFE3"
+}

sciris-3.2.8/docs/_build/html/_static/scripts/bootstrap.js.LICENSE.txt

@@ -0,0 +1,5 @@
+/*!
+  * Bootstrap v5.3.3 (https://getbootstrap.com/)
+  * Copyright 2011-2024 The Bootstrap Authors (https://github.com/twbs/bootstrap/graphs/contributors)
+  * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)
+  */

sciris-3.2.8/docs/_build/html/_static/scripts/fontawesome.js.LICENSE.txt

@@ -0,0 +1,5 @@
+/*!
+ * Font Awesome Free 6.5.2 by @fontawesome - https://fontawesome.com
+ * License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License)
+ * Copyright 2024 Fonticons, Inc.
+ */

sciris-3.2.8/docs/api/_autosummary/sciris.rst

@@ -0,0 +1,48 @@
+sciris
+======
+
+.. automodule:: sciris
+
+   
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+
+
+.. autosummary::
+   :toctree:
+   :template: custom-module-template.rst
+   :recursive:
+   :nosignatures:
+
+   sc_asd
+   sc_colors
+   sc_dataframe
+   sc_datetime
+   sc_fileio
+   sc_math
+   sc_nested
+   sc_odict
+   sc_parallel
+   sc_plotting
+   sc_printing
+   sc_profiling
+   sc_settings
+   sc_utils
+   sc_version
+   sc_versioning
+
+

sciris-3.2.8/docs/api/_autosummary/sciris.sc_asd.asd.rst

@@ -0,0 +1,6 @@
+asd
+===
+
+.. currentmodule:: sciris.sc_asd
+
+.. autofunction:: asd

sciris-3.2.8/docs/api/_autosummary/sciris.sc_asd.rst

@@ -0,0 +1,34 @@
+sc\_asd
+=======
+
+.. automodule:: sciris.sc_asd
+
+   
+   
+   
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+      :toctree:
+      :template: custom-function-template.rst
+      :nosignatures:
+   
+      asd
+   
+   
+
+   
+   
+   
+
+
+
+
+

sciris-3.2.8/docs/api/_autosummary/sciris.sc_colors.alpinecolormap.rst

@@ -0,0 +1,6 @@
+alpinecolormap
+==============
+
+.. currentmodule:: sciris.sc_colors
+
+.. autofunction:: alpinecolormap

sciris-3.2.8/docs/api/_autosummary/sciris.sc_colors.arraycolors.rst

@@ -0,0 +1,6 @@
+arraycolors
+===========
+
+.. currentmodule:: sciris.sc_colors
+
+.. autofunction:: arraycolors

sciris-3.2.8/docs/api/_autosummary/sciris.sc_colors.bandedcolormap.rst

@@ -0,0 +1,6 @@
+bandedcolormap
+==============
+
+.. currentmodule:: sciris.sc_colors
+
+.. autofunction:: bandedcolormap

sciris-3.2.8/docs/api/_autosummary/sciris.sc_colors.bicolormap.rst

@@ -0,0 +1,6 @@
+bicolormap
+==========
+
+.. currentmodule:: sciris.sc_colors
+
+.. autofunction:: bicolormap

sciris-3.2.8/docs/api/_autosummary/sciris.sc_colors.colormapdemo.rst

@@ -0,0 +1,6 @@
+colormapdemo
+============
+
+.. currentmodule:: sciris.sc_colors
+
+.. autofunction:: colormapdemo

sciris-3.2.8/docs/api/_autosummary/sciris.sc_colors.gridcolors.rst

@@ -0,0 +1,6 @@
+gridcolors
+==========
+
+.. currentmodule:: sciris.sc_colors
+
+.. autofunction:: gridcolors

sciris-3.2.8/docs/api/_autosummary/sciris.sc_colors.hex2rgb.rst

@@ -0,0 +1,6 @@
+hex2rgb
+=======
+
+.. currentmodule:: sciris.sc_colors
+
+.. autofunction:: hex2rgb

sciris-3.2.8/docs/api/_autosummary/sciris.sc_colors.hsv2rgb.rst

@@ -0,0 +1,6 @@
+hsv2rgb
+=======
+
+.. currentmodule:: sciris.sc_colors
+
+.. autofunction:: hsv2rgb

sciris-3.2.8/docs/api/_autosummary/sciris.sc_colors.manualcolorbar.rst

@@ -0,0 +1,6 @@
+manualcolorbar
+==============
+
+.. currentmodule:: sciris.sc_colors
+
+.. autofunction:: manualcolorbar

sciris-3.2.8/docs/api/_autosummary/sciris.sc_colors.midpointnorm.rst

@@ -0,0 +1,6 @@
+midpointnorm
+============
+
+.. currentmodule:: sciris.sc_colors
+
+.. autofunction:: midpointnorm

sciris-3.2.8/docs/api/_autosummary/sciris.sc_colors.orangebluecolormap.rst

@@ -0,0 +1,6 @@
+orangebluecolormap
+==================
+
+.. currentmodule:: sciris.sc_colors
+
+.. autofunction:: orangebluecolormap

sciris-3.2.8/docs/api/_autosummary/sciris.sc_colors.parulacolormap.rst

@@ -0,0 +1,6 @@
+parulacolormap
+==============
+
+.. currentmodule:: sciris.sc_colors
+
+.. autofunction:: parulacolormap

sciris-3.2.8/docs/api/_autosummary/sciris.sc_colors.rgb2hex.rst

@@ -0,0 +1,6 @@
+rgb2hex
+=======
+
+.. currentmodule:: sciris.sc_colors
+
+.. autofunction:: rgb2hex

sciris-3.2.8/docs/api/_autosummary/sciris.sc_colors.rgb2hsv.rst

@@ -0,0 +1,6 @@
+rgb2hsv
+=======
+
+.. currentmodule:: sciris.sc_colors
+
+.. autofunction:: rgb2hsv

sciris-3.2.8/docs/api/_autosummary/sciris.sc_colors.rst

@@ -0,0 +1,51 @@
+sc\_colors
+==========
+
+.. automodule:: sciris.sc_colors
+
+   
+   
+   
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+      :toctree:
+      :template: custom-function-template.rst
+      :nosignatures:
+   
+      sanitizecolor
+      shifthue
+      rgb2hex
+      hex2rgb
+      rgb2hsv
+      hsv2rgb
+      vectocolor
+      arraycolors
+      gridcolors
+      midpointnorm
+      manualcolorbar
+      colormapdemo
+      alpinecolormap
+      bicolormap
+      parulacolormap
+      turbocolormap
+      bandedcolormap
+      orangebluecolormap
+   
+   
+
+   
+   
+   
+
+
+
+
+

sciris-3.2.8/docs/api/_autosummary/sciris.sc_colors.sanitizecolor.rst

@@ -0,0 +1,6 @@
+sanitizecolor
+=============
+
+.. currentmodule:: sciris.sc_colors
+
+.. autofunction:: sanitizecolor

sciris-3.2.8/docs/api/_autosummary/sciris.sc_colors.shifthue.rst

@@ -0,0 +1,6 @@
+shifthue
+========
+
+.. currentmodule:: sciris.sc_colors
+
+.. autofunction:: shifthue

sciris-3.2.8/docs/api/_autosummary/sciris.sc_colors.turbocolormap.rst

@@ -0,0 +1,6 @@
+turbocolormap
+=============
+
+.. currentmodule:: sciris.sc_colors
+
+.. autofunction:: turbocolormap

sciris-3.2.8/docs/api/_autosummary/sciris.sc_colors.vectocolor.rst

@@ -0,0 +1,6 @@
+vectocolor
+==========
+
+.. currentmodule:: sciris.sc_colors
+
+.. autofunction:: vectocolor

sciris-3.2.8/docs/api/_autosummary/sciris.sc_dataframe.dataframe.rst

@@ -0,0 +1,45 @@
+dataframe
+=========
+
+.. currentmodule:: sciris.sc_dataframe
+
+.. autoclass:: dataframe
+   :members:
+   :show-inheritance:
+   :special-members: __call__, __add__, __mul__
+
+   
+   
+   .. rubric:: Attributes
+
+   .. autosummary::
+   
+      ~dataframe.T
+      ~dataframe.at
+      ~dataframe.attrs
+      ~dataframe.axes
+      ~dataframe.cols
+      ~dataframe.columns
+      ~dataframe.dtypes
+      ~dataframe.empty
+      ~dataframe.flags
+      ~dataframe.iat
+      ~dataframe.iloc
+      ~dataframe.index
+      ~dataframe.loc
+      ~dataframe.ncols
+      ~dataframe.ndim
+      ~dataframe.nrows
+      ~dataframe.shape
+      ~dataframe.size
+      ~dataframe.style
+      ~dataframe.values
+   
+   
+
+   
+   
+   .. rubric:: Methods
+
+   
+   

sciris-3.2.8/docs/api/_autosummary/sciris.sc_dataframe.rst

@@ -0,0 +1,34 @@
+sc\_dataframe
+=============
+
+.. automodule:: sciris.sc_dataframe
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Classes
+
+   .. autosummary::
+      :toctree:
+      :template: custom-class-template.rst
+      :nosignatures:
+   
+      dataframe
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+
+
+