Post1.4.1

.github/workflows/build-test.yml

@@ -18,12 +18,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
         os: [ubuntu-latest, windows-latest, macos-latest]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: "pip: Python ${{ matrix.python-version }} / ${{ matrix.os }}"
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

.github/workflows/coverage.yml

@@ -14,11 +14,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.10" ]
+        python-version: [ "3.11" ]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: "pip: Python ${{ matrix.python-version }} coverage"
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -32,5 +32,7 @@ jobs:
       run: |
         python -m pytest
     - name: Upload
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
       run: |
         bash <(curl -s https://codecov.io/bash) -Z

.github/workflows/draft-pdf.yml

@@ -8,14 +8,14 @@ jobs:
     name: Paper Draft
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Build draft PDF
         uses: openjournals/openjournals-draft-action@master
         with:
           journal: joss
           paper-path: paper/paper.md
       - name: Upload
-        uses: actions/upload-artifact@v1
+        uses: actions/upload-artifact@v4
         with:
           name: paper
           path: paper/paper.pdf

.github/workflows/mpi-test.yml

@@ -14,11 +14,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.11"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: "pip: Python ${{ matrix.python-version }}"
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies

.github/workflows/pypi-release.yml

@@ -10,7 +10,7 @@ jobs:
     if: "!contains(github.event.head_commit.message, 'Bump version')"
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         persist-credentials: false
     - name: current_version

LICENCE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright © 2017-2023 Andrew P Smith
+Copyright © 2017-2024 Andrew P Smith
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

docs/api.md

@@ -7,4 +7,4 @@
 
 ## Type stubs
 
-Type stubs were generated for the core C++ library using the `pybind11-stubgen` package, although significant editing of the output was required. See `__init__.pyi` for details.
+Type stubs were generated for the core C++ library using the `pybind11-stubgen` package, with minor manual corrections. See `__init__.pyi` for details.

docs/developer.md

@@ -90,7 +90,7 @@ The script from [codecov.io](https://codecov.io/gh/virgesmith/neworder/) uses `g
 
 ## Generating type stubs
 
-Type stubs can be generated for the C++ module using `pybind11-stubgen`, although manual modifications are needed for the output (e.g. docstrings for overloaded functions are misplaced, numpy types need to be fixed).
+Type stubs can be generated for the C++ module using `pybind11-stubgen`, although manual modifications may be needed, plus numpy types need to be fixed globally.
 
 ```sh
 pybind11-stubgen _neworder_core --ignore-invalid all

docs/examples/boids.md

@@ -22,33 +22,22 @@ Each entity travels at a fixed speed in a 2- or 3-dimensional constrained univer
 
 (if a separation is required, the boid will not attempt to align or cohere)
 
-The entities are stored in a pandas `DataFrame` and use `neworder.Space` to update positions. There are no explicit `for` loops in the model - all position and velocity calculations are "vectorised"<sup>&ast;</sup> for efficiency.
+The entities are stored in a pandas `DataFrame` and use `neworder.Space` to update positions. There are no explicit `for` loops in the model - all position and velocity calculations are "vectorised"[^1] for efficiency.
 
-&ast; in this context "vectorisation" merely means the avoidance of explicit loops in an interpreted language. The actual implementation may be compiled to assembly language, vectorised in the true ([SIMD](https://en.wikipedia.org/wiki/SIMD)) sense, parallelised, optimised in other ways, or any combination thereof.
+[^1]: in this context "vectorisation" merely means the avoidance of explicit loops in an interpreted language. The actual implementation may be compiled to assembly language, vectorised in the true ([SIMD](https://en.wikipedia.org/wiki/SIMD)) sense, parallelised, optimised in other ways, or any combination thereof.
 
 Run like so
 
 ```sh
 python examples/boids/run.py 2d
 ```
-
-The 2d version utilises a wrap-around domain and does not implement the reversion step.
-
 or
 
 ```sh
 python examples/boids/run.py 3d
 ```
 
-which runs
-
-{{ include_snippet("examples/boids/run.py") }}
-
-and this is the 3-d implementation:
-
-{{ include_snippet("examples/boids/boids3d.py") }}
-
-A 2-d implementation is also provided in `examples/boids/boids2d.py`.
+The 2d version utilises a wrap-around domain and so does not require the reversion step.
 
 ## Outputs
 

docs/examples/mortality.md

@@ -1,6 +1,6 @@
 # Mortality
 
-We implement the example *The Life Table* from the second chapter of the book *Microsimulation and Population Dynamics* [[3]](#references). It models mortality in a homogeneous population with an age-specific mortality rate.
+We implement the example *The Life Table* from the second chapter of the book *Microsimulation and Population Dynamics* [[3]](../references.md). It models mortality in a homogeneous population with an age-specific mortality rate.
 
 This example implements the model in two different ways: firstly a discrete case-based microsimulation, and again using a continuous sampling methodology, showcasing how the latter can be much more efficient. Rather than having a class to represent an individual, as would be standard in a MODGEN implementation, individuals are stored in a *pandas* `Dataframe` which provides fast iteration over the population.
 

docs/examples/people.md

@@ -6,7 +6,7 @@
 
 In this example, the input data is a csv file containing a microsynthesised 2011 population of Newcastle generated from UK census data, by area (MSOA), age, gender and ethnicity. The transitions modelled are: ageing, births, deaths and migrations, over a period of 40 years to 2051.
 
-Births, deaths and migrations (applied in that order) are modelled using Monte-Carlo simulation (sampling Poisson processes in various ways) using distributions parameterised by age, sex and ethnicity-specific fertility, mortality and migration rates respectively, which are largely fictitious (but inspired by data from the NewETHPOP[[1]](#references.md) project).
+Births, deaths and migrations (applied in that order) are modelled using Monte-Carlo simulation (sampling Poisson processes in various ways) using distributions parameterised by age, sex and ethnicity-specific fertility, mortality and migration rates respectively, which are largely fictitious (but inspired by data from the NewETHPOP[[1]](../references.md) project).
 
 For the fertility model newborns simply inherit their mother's location and ethnicity, are born aged zero, and have a randomly selected gender (with even probability). The migration model is an 'in-out' model, i.e. it is not a full origin-destination model. Flows are either inward from 'elsewhere' or outward to 'elsewhere'.
 

docs/examples/riskpaths.md

@@ -1,6 +1,6 @@
 # RiskPaths
 
-RiskPaths is a well-known MODGEN model that is primarily used for teaching purposes and described here[[5]](#references) in terms of the model itself and here in terms of implementation[[6]](#references). It models fertility in soviet-era eastern Europe, examining fertility as a function of time and union state. In the model, a woman can enter a maximum of two unions in her lifetime. The first union is divided into two sections: a (deterministic) 3 year period during which fertility is at a maximum, followed by a (stochastic) period with lower fertility.
+RiskPaths is a well-known MODGEN model that is primarily used for teaching purposes and described here[[5]](../references.md) in terms of the model itself and here in terms of implementation[[6]](../references.md). It models fertility in soviet-era eastern Europe, examining fertility as a function of time and union state. In the model, a woman can enter a maximum of two unions in her lifetime. The first union is divided into two sections: a (deterministic) 3 year period during which fertility is at a maximum, followed by a (stochastic) period with lower fertility.
 
 ![riskpaths](./img/riskpaths.png)
 

docs/macros.py

@@ -1,90 +1,109 @@
 # macros for mkdocs-macros-plugin
-import os
-import requests
 import importlib
+import os
 from datetime import datetime
+from functools import cache
+from typing import Any
+
+import requests
 
 _inline_code_styles = {
-  ".py": "python",
-  ".sh": "bash",
-  ".h": "cpp",
-  ".cpp": "cpp",
-  ".c": "c",
-  ".rs": "rs",
-  ".js": "js",
-  ".md": None
+    ".py": "python",
+    ".sh": "bash",
+    ".h": "cpp",
+    ".cpp": "cpp",
+    ".c": "c",
+    ".rs": "rs",
+    ".js": "js",
+    ".md": None,
 }
 
 # this is the overall record id, not a specific version
-_NEWORDER_ZENODO_ID = 4031821
+_NEWORDER_ZENODO_ID = 4031821  # search using this (or DOI 10.5281/zenodo.4031821) just doesnt work
+
+
+@cache
+def get_zenodo_record() -> dict[str, Any]:
+    try:
+        response = requests.get(
+            "https://zenodo.org/api/records",
+            params={
+                "q": "(virgesmith) AND (neworder)",  # this is the only query that seems to work
+                "access_token": os.getenv("ZENODO_PAT"),
+            },
+        )
+        response.raise_for_status()
+        # with open("zenodo-result.json", "w") as fd:
+        #     fd.write(response.text)
+        return response.json()["hits"]["hits"][0]
+    except Exception as e:
+        return {f"{e.__class__.__name__}": f"{e} while retrieving zenodo record"}
 
 
 def write_requirements() -> None:
-  try:
-    with open("docs/requirements.txt", "w") as fd:
-      fd.write(f"""# DO NOT EDIT
+    try:
+        with open("docs/requirements.txt", "w") as fd:
+            fd.write(
+                f"""\
+# DO NOT EDIT
 # auto-generated @ {datetime.now()} by docs/macros.py::write_requirements()
 # required by readthedocs.io
-""")
-      fd.writelines(f"{dep}=={importlib.metadata.version(dep)}\n" for dep in [
-        "mkdocs",
-        "mkdocs-macros-plugin",
-        "mkdocs-material",
-        "mkdocs-material-extensions",
-        "mkdocs-video",
-        "requests"
-      ])
-  # ignore any error, this should only run in a dev env anyway
-  except:
-    pass
+"""
+            )
+            fd.writelines(
+                f"{dep}=={importlib.metadata.version(dep)}\n"
+                for dep in [
+                    "mkdocs",
+                    "mkdocs-macros-plugin",
+                    "mkdocs-material",
+                    "mkdocs-material-extensions",
+                    "mkdocs-video",
+                    "requests",
+                ]
+            )
+    # ignore any error, this should only run in a dev env anyway
+    except:  # noqa: E722
+        pass
 
 
 def define_env(env):
+    @env.macro
+    def insert_zenodo_field(*keys: str) -> Any:
+        result = get_zenodo_record()
+        for key in keys:
+            result = result[key]
+        return result
 
-  @env.macro
-  def insert_zenodo_field(*keys: str):
-    """ This is the *released* version not the dev one """
-    try:
-      response = requests.get('https://zenodo.org/api/records', params={'q': _NEWORDER_ZENODO_ID, 'access_token': os.getenv("ZENODO_PAT")})
-      response.raise_for_status()
-      result = response.json()["hits"]["hits"][0]
-      for k in keys:
-        result = result[k]
-      return result
+    @env.macro
+    def include_snippet(filename, tag=None, show_filename=True):
+        """looks for code in <filename> between lines containing "!<tag>!" """
+        full_filename = os.path.join(env.project_dir, filename)
 
-    except Exception as e:
-      return f"{e.__class__.__name__}:{e} while retrieving {keys}"
-
-
-  @env.macro
-  def include_snippet(filename, tag=None, show_filename=True):
-    """ looks for code in <filename> between lines containing "!<tag>!" """
-    full_filename = os.path.join(env.project_dir, filename)
-
-    _, file_type = os.path.splitext(filename)
-    # default to literal "text" for inline code style
-    code_style = _inline_code_styles.get(file_type, "text")
-
-    with open(full_filename, 'r') as f:
-      lines = f.readlines()
-
-    if tag:
-      tag = f"!{tag}!"
-      span = []
-      for i, l in enumerate(lines):
-        if tag in l:
-          span.append(i)
-      if len(span) != 2:
-        return f"```ERROR {filename} ({code_style}) too few/many tags ({len(span)}) for '{tag}'```"
-      lines = lines[span[0] + 1: span[1]]
-
-    if show_filename:
-      footer = f"\n[file: **{filename}**]\n"
-    else:
-      footer = ""
-    if code_style is not None:
-      return f"```{code_style}\n{''.join(lines)}```{footer}"
-    else:
-      return "".join(lines) + footer
-
-write_requirements()
+        _, file_type = os.path.splitext(filename)
+        # default to literal "text" for inline code style
+        code_style = _inline_code_styles.get(file_type, "text")
+
+        with open(full_filename, "r") as f:
+            lines = f.readlines()
+
+        if tag:
+            tag = f"!{tag}!"
+            span = []
+            for i, line in enumerate(lines):
+                if tag in line:
+                    span.append(i)
+            if len(span) != 2:
+                return f"```ERROR {filename} ({code_style}) too few/many tags ({len(span)}) for '{tag}'```"
+            lines = lines[span[0] + 1 : span[1]]
+
+        if show_filename:
+            title = f'title="{filename}"'
+        else:
+            title = ""
+        if code_style is not None:
+            return f"```{code_style} {title}\n{''.join(lines)}```"
+        else:
+            return "".join(lines)
+
+
+# write_requirements()