Merge pull request #51 from GavinHuttley/main

Maint

Author: GavinHuttley

.github/workflows/ci.yml

@@ -47,7 +47,7 @@ jobs:
           lname="snx-${{matrix.os}}-${{matrix.python-version}}.lcov"
           xname="snx-${{matrix.os}}-${{matrix.python-version}}.xml"
           cov="lcov -o$lname xml -o$xname"
-          uv run --group test nox --force-python python -s testcov -- $cov
+          uv run --group dev nox --force-python python -s testcov -- $cov
 
       - name: Coveralls Parallel
         uses: coverallsapp/github-action@v2
@@ -83,7 +83,7 @@ jobs:
 
       - name: "Run Type Checking for ${{ matrix.python-version }}"
         run: |
-          uv run --group test nox --force-python python -s type_check
+          uv run --group dev nox --force-python python -s type_check
 
   finish:
     name: "Finish Coveralls"

README.md

@@ -4,7 +4,7 @@
 
 [![Coverage Status](https://coveralls.io/repos/github/cogent3/scinexus/badge.svg?branch=main)](https://coveralls.io/github/cogent3/scinexus?branch=main) [![Codacy Badge](https://app.codacy.com/project/badge/Grade/fd8810efd4f142069bd84144e14350b4)](https://app.codacy.com/gh/cogent3/scinexus/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade) [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) [![CI](https://github.com/cogent3/scinexus/actions/workflows/ci.yml/badge.svg)](https://github.com/cogent3/scinexus/actions/workflows/ci.yml)
 
-*`scinexus` is a framework for rapid development of data processing applications. It enables interoperability between objects through defined data types, allowing development of scientific domain app ecosystems. What `dataclasses` and `attrs` do for declaring data, `scinexus` does for declaring algorithms.*
+*`scinexus` is a framework for rapid development of data processing applications. It enables interoperability between objects through defined data types, allowing development of scientific domain app ecosystems. Just as `attrs` and `dataclasses` use type hints to simplify data type definition, `scinexus` uses them to simplify writing best-practice scientific algorithms.*
 
 Many scientific problems require repeating calculations across many files or database records. Such tasks suit data-level parallelism, but writing robust, maintainable code for them is often tedious and quickly becomes complex.
 

docs/explanation/why-composable-apps.md

@@ -16,9 +16,9 @@ As the robustness of POSIX based operating systems (think Linux, Mac OS, Unix) c
 
 **`scinexus` encourages this design pattern.** We leverage the Python type annotation system to govern the compatibility (composability) of different applications. This enables in-process composition of your applications with validation of the consistency of the pipeline and the consistency of the data being run through it.
 
-We can expand on this slightly for the problem of scientific computation by considering the critical benchmark of satisfying the conditions for reproducibile computation, i.e. the obligation to track all of the properties affecting the execution of your algorithm. Examples of this are the operating system, the language version, the seed used for the random number generator, etc.
+We can expand on this slightly for the problem of scientific computation by considering the critical benchmark of satisfying the conditions for reproducible computation, i.e. the obligation to track all of the properties affecting the execution of your algorithm. Examples of this are the operating system, the language version, the seed used for the random number generator, etc.
 
-**`scinexus` does this for you.** For example, we intercept all arguments (including default values) passed to the construction of apps and record them so that the app state is logged. If you, the developer, also leverage the capabilities of the [`scitrack`](https://pypi.org/project/scitrack/) logging package (which `scinexus` has as a dependency), you can capture extra information such as versions of packages that your application depends on. We provide an [example][leveraging-scitrack-for-reproducibility] of using `scitrack` for these cases.
+**`scinexus` does this for you.** For example, we intercept all arguments (including default values) passed to the construction of apps and record them so that the app state is logged. If you, the developer, also leverage the capabilities of the [`scitrack`](https://pypi.org/project/scitrack/) logging package (which `scinexus` has as a dependency), you can capture extra information such as versions of packages that your application depends on. We provide an [example](../howto/log-and-cite.md#leveraging-scitrack-for-reproducibility) of using `scitrack` for these cases.
 
 ## Improve the accessibility of your work for end users
 

docs/howto/handle-failures.md

@@ -89,7 +89,7 @@ exec_codeblock(src=src, max_lines=4, admonition='???- example "Example"')
     # NotCompleted(type=ERROR, origin=load_aligned, source="primate_brca1",
     # message="Traceback (most recent call last):   File
     # "/Users/gavin/repos/SciNexus/src/scinexus/composable.py", line 545, in __call__
-    # result = self.main(val, *args, **kwargs)   File [...]
+    # result = self.main(val, *args, **kwargs) [...]
     ```
 <!-- [[[end]]] -->
 

docs/howto/run-in-parallel.md

@@ -145,7 +145,7 @@ On systems with multiple nodes (e.g. an HPC cluster), use MPI via the [mpi4py](h
 pip install mpi4py
 ```
 
-or installing `scinexus` [with `mpi` extra][optional-extras].
+or installing `scinexus` [with `mpi` extra](../install.md#optional-extras).
 
 Set the backend to MPI:
 

docs/index.md

@@ -5,7 +5,7 @@
 
 # About
 
-!!! abstract "*What `dataclasses` and `attrs` do for declaring data, `scinexus` does for declaring algorithms.*"
+!!! abstract "*Just as `attrs` and `dataclasses` use type hints to simplify data type definition, `scinexus` uses them to simplify writing best-practice scientific algorithms.*"
 
 `scinexus` (pronounced 'sigh-nexus') is a Python framework for rapid development of data processing applications. It enables interoperability between apps through defined data types, allowing development of scientific domain app ecosystems (for examples see [cogent3](https://cogent3.org/doc/app/index-app.html) and [piqtree](https://piqtree.readthedocs.io/en/stable/)).
 

docs/tutorials/composing-apps.md

@@ -159,13 +159,13 @@ annotations=[
     # NotCompleted(type=ERROR, origin=load_aligned, source="primate_brca1",
     # message="Traceback (most recent call last):   File
     # "/Users/gavin/repos/SciNexus/src/scinexus/composable.py", line 545, in __call__
-    # result = self.main(val, *args, **kwargs)   File
-    # "/Users/gavin/repos/SciNexus/.venv/lib/python3.14/site-
+    # result = self.main(val, *args, **kwargs)
+    # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File
+    # "/Users/gavin/repos/SciNexus/.venv/lib/python3.12/site-
     # packages/cogent3/app/io.py", line 334, in main     return _load_seqs(path,
-    # cogent3.make_aligned_seqs, self._parser, self.moltype)   File
-    # "/Users/gavin/repos/SciNexus/.venv/lib/python3.14/site-
-    # packages/cogent3/app/io.py", line 294, in _load_seqs     data = _read_it(path)
-    # File [...]
+    # cogent3.make_aligned_seqs, self._parser, self.moltype)
+    # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File
+    # "/Users/gavin/repos/SciNexus/.venv/lib/python3.12/site- [...]
     ```
 
     1. An error during load — `select_seqs` is never called.

noxfile.py

@@ -23,26 +23,26 @@ def fmt(session: nox.Session) -> None:
 
 @nox.session(python="3.14")
 def cogdocs(session: nox.Session) -> None:
-    session.install("-e", ".", "--group", "test")
-    cmnd = 'find docs -name "*.md" | xargs uv run --group test cog -r -I docs/scripts'
+    session.install("-e", ".", "--group", "dev")
+    cmnd = 'find docs -name "*.md" | xargs uv run --group dev cog -r -I docs/scripts'
     subprocess.run(cmnd, check=True, shell=True)  # noqa: S602
 
 
 @nox.session(python=[f"3.{v}" for v in _py_versions])
 def type_check(session):
-    session.install("-e", ".", "--group", "test")
+    session.install("-e", ".", "--group", "dev")
     session.run("mypy", "src/scinexus/")
 
 
 @nox.session(python=[f"3.{v}" for v in _py_versions])
 def test_types(session):
-    session.install("-e", ".", "--group", "test")
+    session.install("-e", ".")
     session.run("mypy", "src/scinexus/")
 
 
 @nox.session(python=[f"3.{v}" for v in _py_versions])
 def test(session):
-    session.install("-e", ".", "--group", "test")
+    session.install("-e", ".", "--group", "dev")
     session.run("uv", "pip", "list")
     # doctest modules within scinexus
     session.chdir("src/scinexus")
@@ -67,7 +67,7 @@ def test(session):
 
 @nox.session(python=[f"3.{v}" for v in _py_versions])
 def testmpi(session):
-    session.install("-e", ".[mpi]", "--group", "test")
+    session.install("-e", ".[mpi]")
     session.chdir("tests")
     py = pathlib.Path(session.bin_paths[0]) / "python"
     session.run(
@@ -91,7 +91,7 @@ def testmpi(session):
 
 @nox.session(python=[f"3.{v}" for v in _py_versions])
 def testcov(session):
-    session.install("-e", ".", "--group", "test")
+    session.install("-e", ".", "--group", "dev")
     cover_mpi = shutil.which("mpiexec") is not None
     if cover_mpi:
         session.install("-e", ".[mpi]")
@@ -162,7 +162,7 @@ def testcov(session):
 
 @nox.session(python=[f"3.{v}" for v in _py_versions])
 def test_docs(session):
-    session.install("-e", ".", "--group", "test")
+    session.install("-e", ".", "--group", "dev")
     session.run("uv", "pip", "list")
     # doctest modules within scinexus
     session.chdir("docs")

pyproject.toml

@@ -38,7 +38,7 @@ mpi = ["mpi4py"]
 rich = ["rich"]
 
 [dependency-groups]
-test = [
+dev = [
     "pymdown-extensions>=10.21.2",
     "zensical>=0.0.33",
     "cogent3[extra]>=2026.4.20a0",

src/scinexus/_version.py

@@ -1 +1 @@
-__version__ = "2026.4.25b0"
+__version__ = "2026.4.25"