stdferdowsim 0.1.0__tar.gz

stdferdowsim-0.1.0/.github/ISSUE_TEMPLATE/bug-report-issue-template.md

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+---
+name: Bug report
+about: A problem with stdvoidsim
+title:
+labels:
+assignees: ''
+
+---
+
+*This template is a suggestion that may not fit your issue: delete/modify anything!*
+
+**Short description of the problem:**
+*Describe what you are doing, what you think should happen, and what actually happens.*
+
+**How to reproduce the problem:**
+*If possible, post code (a [minimal working example](https://en.wikipedia.org/wiki/Minimal_working_example))
+that reproduces the problem.*
+
+**Suggested fixes:**
+*If you have an idea of what's causing the problem or how to fix it, we'd like to hear it!*

stdferdowsim-0.1.0/.github/ISSUE_TEMPLATE/dfe-qc-issue-template.md

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+---
+name: DFE QC issue template
+about: Quality control process for DFE addition
+title: QC for {dfe_id} ({species})
+labels: DFE QC
+assignees: ''
+
+---
+
+**PR for new model:** {link to Pull Request}
+**Original paper:** {ink to original paper}
+**Parameter values:** {reference to where parameter values can be found}
+
+**Potential issues that might lead to differences between the model implementations:**
+{description of any potential issues}
+
+**QC'er requests:** {tag potential developers to QC the model}

stdferdowsim-0.1.0/.github/ISSUE_TEMPLATE/feature-request-issue-template.md

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+---
+name: Feature request
+about: A suggestion for something to add to stdvoidsim.
+title:
+labels: enhancement
+assignees: ''
+
+---
+
+*This template is a suggestion that may not fit your issue: delete/modify anything!*
+
+**Short description of what you'd like added:**
+*Describe briefly how you think stdvoidsim could be better.*
+
+**Rationale and considerations:**
+*Give some more explanation of why this is a good idea,
+and what considerations there are in implementing it.
+For instance: if you're suggesting that a new species, model, or map is added
+then say who'd use the resource.
+Or, if you're suggesting a new method in the API,
+talk through the proposed arguments to the method and outputs.*

stdferdowsim-0.1.0/.github/ISSUE_TEMPLATE/model-qc-issue-template.md

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+---
+name: Model QC issue template
+about: Quality control process for model addition
+title: QC for {model_id} ({species})
+labels: Model QC
+assignees: ''
+
+---
+
+**PR for new model:** {link to Pull Request}
+**Original paper:** {ink to original paper}
+**Parameter values:** {reference to where parameter values can be found}
+**Population indices:** {description of population indices}
+
+**Potential issues that might lead to differences between the model implementations:**
+{description of any potential issues}
+
+**QC'er requests:** {tag potential developers to QC the model}

stdferdowsim-0.1.0/.github/ISSUE_TEMPLATE/new-species-issue-template.md

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+---
+name: New species
+about: Adding a new species to the stdvoidsim catalogue.
+title:
+labels: enhancement
+assignees: ''
+
+---
+
+- **Name:** scientific name of the species
+- **Common name:**
+
+**Description:** any other discussion or useful background? (optional)
+
+*Note: Maybe you don't know a lot of the things below - but, that's OK!
+The criteria are that (a) the choice is reasonable, and (b) the rationale is clear.
+What we want is a "reasonable estimate" (or, "best guess") - if you were to use a number in a paper,
+what would you use and how would you justify it to your collaborators?
+For instance, for "generation time", best would be to cite a paper that actually measures
+or estimates generation time. But most species don't have this;
+next best would be to give a number used in the literature, and provide a citation that used it
+(and hopefully the publication gives a justification also).
+Lacking this, you might provide a number from a related species (and a citation for this).*
+
+*Here is the checklist of things that we need to add a species to the catalogue.
+Each thing should be provided, with a justification (maybe short) and a citation.*
+
+**Demographic information:**
+
+- [] generation time in years
+- [] "default" population size
+
+
+**Chromosome structure:**
+
+*Note:* The assembly should be *chromosome-level*, i.e., not composed of thousands of scaffolds.
+
+- [] ensembl assembly ID *or*, if the assembly is not in Ensembl, a list of chromosomes with *name* and *length* (in bp)
+
+*Note: species in Ensembl can be found in one of these lists:
+[vertebrates](https://uswest.ensembl.org/info/about/species.html),
+["metazoa"](https://metazoa.ensembl.org/species.html),
+[plants](https://plants.ensembl.org/species.html),
+[fungi](https://fungi.ensembl.org/species.html),
+[protists](http://protists.ensembl.org/species.html),
+or [bacteria](http://bacteria.ensembl.org/species.html).*
+
+
+**Recombination rates:**
+
+- [] genetic map of recombination rates (as a hapmap or csv file)
+- [] genome-wide mean recombination rate (which will be used as the default)
+
+
+**Mutation rate:**
+
+- [] genome-wide mean mutation rate
+
+
+**Demographic model:**
+
+- [] as a list of population sizes, growth rates, migration rates, etcetera. **(optional)**
+- [] citation
+
+
+**Other information:**
+
+These are things we don't currently use, but will want to use in the future:
+
+- [] sex determination system, and which chromosomes are the sex chromosome(s)
+- [] ploidy

stdferdowsim-0.1.0/.github/ISSUE_TEMPLATE/species-qc-issue-template.md

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+---
+name: Species QC issue template
+about: Quality control process for species addition
+title: QC for {species}
+labels: Species QC
+assignees: ''
+
+---
+
+**PR for new species:** {link to Pull Request}
+
+If you volunteer to QC this species, please use the checklist below.
+While this list is intended to be comprehensive, it may not be exhaustive.
+Where relevant, the QC reviewer should identify that parameter values match
+those given in the linked citation(s).
+
+The QC reviewer should start a pull request that fills out the test stubs
+with independently obtained values. The reviewer may look at the python code
+for rationale provided in comments, but should ignore the actual code
+as much as possible - comments in the code should give enough information
+that it's obvious how to get the correct value from the provided references.
+(In particular, we shouldn't copy-paste the value from the code into the test!)
+
+- [ ] Recombination rate.
+  - This might be genome-wide, or per-chromosome. Both are fine.
+  - Check there's a comment describing where it came from, and/or how calculated.
+  - From a publication? Check the value(s) match the publication.
+  - Calculated somehow? Average over a recombination/genetic map? Redo the calculation.
+- [ ] Mutation rate.
+  - This might be genome-wide, or per-chromosome. Both are fine.
+  - Check there's a comment describing where it came from, and/or how calculated.
+  - From a publication? Check the value(s) match the publication.
+  - Calculated somehow? Redo the calculation.
+- [ ] Recombination/genetic map (if present).
+  - Does it match the assembly? Liftover is fine, if clearly stated.
+  - Is the description/long_description a good summary of how the map was created?
+- [ ] Population size.
+- [ ] Generation time.
+
+For each citation, check:
+- Doi link.
+- Is publication a preprint? Is there a peer-reviewed publication instead?
+- Is the year correct.
+- Is the author correct (spelling, accents/ligatures/etc.)
+
+Citations are required for:
+- [ ] Genome reference assembly.
+- [ ] Mutation rate.
+- [ ] Recombination rate.
+- [ ] Recombination/genetic map(s) (if relevant).
+- [ ] Population size.
+- [ ] Generation time.
+
+The final PR should:
+- [ ] fill out the test stubs
+- [ ] delete the `pytest.mark.skip` lines that make the tests not run
+- [ ] make sure they pass, talking to the original author to figure out discrepancies

stdferdowsim-0.1.0/.github/dependabot.yml

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+version: 2
+updates:
+- package-ecosystem: pip
+  directory: "/requirements/CI"
+  schedule:
+    interval: weekly
+  open-pull-requests-limit: 10

stdferdowsim-0.1.0/.github/mergify.yml

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+queue_rules:
+  - name: default
+    conditions:
+      - base=main
+      - check-success=build-deploy-docs
+      - check-success=pre-commit
+      - check-success=tests (ubuntu-20.04, 3.7)
+      - check-success=tests (ubuntu-20.04, 3.10)
+      - check-success=tests (macos-11, 3.7)
+      - check-success=tests (macos-11, 3.10)
+      - check-success=tests (windows-latest, 3.7)
+      - check-success=tests (windows-latest, 3.10)
+      - check-success=codecov/patch
+      - check-success=codecov/project
+
+pull_request_rules:
+  - name: automatic merge for Dependabot pull requests
+    conditions:
+      - base=main
+      - author~=^dependabot(|-preview)\[bot\]$
+      - label=dependencies
+      - check-success=build-deploy-docs
+      - check-success=pre-commit
+      - check-success=tests (ubuntu-20.04, 3.7)
+      - check-success=tests (ubuntu-20.04, 3.10)
+      - check-success=tests (macos-10.15, 3.7)
+      - check-success=tests (macos-10.15, 3.10)
+      - check-success=tests (windows-latest, 3.7)
+      - check-success=tests (windows-latest, 3.10)
+      - check-success=codecov/patch
+      - check-success=codecov/project
+    actions:
+      queue:
+        name: default

stdferdowsim-0.1.0/.github/workflows/docs.yml

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+name: Build and deploy docs
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+    tags:
+      - '*'
+
+# Allow the deploy job to write to the repo (e.g. gh-pages).
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Only one concurrent deployment
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+  # Only run in the main repo; skip in forks or other repos (e.g. stdvoidsim-docs) to avoid 404 on checkout.
+  build:
+    if: github.repository == 'kevinkorfmann/stdvoidsim'
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install deps
+        run: |
+          python -m pip install wheel
+          python -m pip install -r requirements/CI/requirements.txt
+          python -m pip install .
+
+      - name: Build Docs
+        run: make -C docs
+
+      - name: Upload artifact
+        if: (!github.event.pull_request)
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/_build/html
+
+  # Uncomment the deploy job and enable Pages (Settings → Pages → Source: GitHub Actions) to publish docs.
+  # deploy:
+  #   if: (!github.event.pull_request) && github.repository == 'kevinkorfmann/stdvoidsim'
+  #   needs: build
+  #   runs-on: ubuntu-24.04
+  #   environment:
+  #     name: github-pages
+  #     url: ${{ steps.deploy.outputs.page_url }}
+  #   steps:
+  #     - id: deploy
+  #       uses: actions/deploy-pages@v4

stdferdowsim-0.1.0/.github/workflows/pre-commit.yml

@@ -0,0 +1,17 @@
+name: pre-commit
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+      - uses: pre-commit/action@v3.0.1

stdferdowsim-0.1.0/.github/workflows/publish-pypi.yml

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+# Publish stdferdowsim to PyPI when a version tag (v*.*.*) is pushed.
+# Uses PyPI Trusted Publishing (OIDC); no API token needed.
+# Configure the publisher at https://pypi.org/manage/project/stdferdowsim/settings/publishing/
+# Then: git tag v0.1.0 && git push origin v0.1.0
+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - "v*.*.*"
+
+jobs:
+  build-and-publish:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write  # required for Trusted Publishing
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # needed for setuptools_scm to get version from tag
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+
+      - name: Build package
+        run: python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

stdferdowsim-0.1.0/.github/workflows/tests.yml

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+name: tests
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  tests:
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-24.04, macos-latest, windows-latest]
+        python: ["3.10", "3.12"]
+    env:
+      CONDA_ENV_NAME: stdvoidsim
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
+    steps:
+      - name: cancel previous runs
+        uses: styfle/cancel-workflow-action@0.12.1
+        with:
+          access_token: ${{ github.token }}
+
+      - name: checkout
+        uses: actions/checkout@v4.2.2
+
+      - name: Cache conda and dependencies
+        id: cache
+        uses: actions/cache@v4.2.0
+        env:
+          # Increase this to reset the cache if the key hasn't changed.
+          CACHE_NUM: 0
+        with:
+          path: ${{ env.CONDA }}/envs
+          key: ${{ runner.os }}-${{ runner.arch }}-${{ matrix.python}}-conda-${{ env.CACHE_NUM }}-${{ hashFiles('requirements/CI/*') }}
+
+      - name: Install Conda
+        uses: conda-incubator/setup-miniconda@v3.1.0
+        if: steps.cache.outputs.cache-hit != 'true'
+        with:
+          activate-environment: anaconda-client-env
+          python-version: ${{ matrix.python }}
+          channels: conda-forge
+          channel-priority: strict
+          auto-update-conda: true
+
+      - name: Fix windows .profile
+        if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest'
+        run: |
+          cp ~/.bash_profile ~/.profile
+
+      - name: Install conda deps
+        if: steps.cache.outputs.cache-hit != 'true'
+        shell: bash -l {0} #We need a login shell to get conda
+        run: |
+          conda install --yes --file=requirements/CI/conda.txt
+
+      - name: Install pip deps
+        if: steps.cache.outputs.cache-hit != 'true'
+        shell: bash -l {0}
+        run: |
+            pip install -r requirements/CI/requirements.txt
+
+      - name: run test suite
+        run: |
+          source ~/.profile
+          conda activate anaconda-client-env
+          python -m pytest \
+            -n 0 \
+            -v \
+            --cov=stdvoidsim \
+            --cov-branch \
+            --cov-report=term-missing \
+            --cov-report=xml \
+            tests
+
+      - name: upload coverage report to codecov
+        uses: codecov/codecov-action@v5.1.1
+        with:
+          fail_ci_if_error: true
+          env_vars: OS,PYTHON
+          # Use upload token to avoid upload failures.
+          # https://github.com/codecov/codecov-action/issues/837
+          token: 8ae76ade-9d0e-4a2d-b9ef-1180235be07f

stdferdowsim-0.1.0/.gitignore

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+__pycache__
+stdferdowsim/_version.py
+docs/_build
+docs/parameter_images
+.*.swp
+build
+dist
+stdvoidsim.egg-info
+.coverage
+htmlcov
+_test_cache
+test_cache
+.manuscript
+.test/*
+!.test/run_slim_test.py
+!.test/run_simulation.py
+!.test/README.txt
+!.test/run_cli_test.sh
+!.test/install_and_run.sh
+*.pyc

stdferdowsim-0.1.0/.readthedocs.yml

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+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "mambaforge-23.11"
+  jobs:
+    post_checkout:
+      - git fetch --unshallow || true
+
+sphinx:
+  builder: html
+  configuration: docs/conf.py
+  fail_on_warning: false
+
+conda:
+  environment: requirements/rtd-conda-environment.yml
+
+python:
+  # Install the local package using pip so that stdferdowsim is in the path.
+  install:
+    - method: pip
+      path: .

stdferdowsim-0.1.0/.test/README.txt

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+stdvoidsim – install and use (hidden test dir)
+
+Install (from repo root):
+  pip install -e .
+
+  Or use the script (creates .test/venv and installs there):
+  .test/install_and_run.sh
+
+Use (Python):
+  import stdvoidsim
+  species = stdvoidsim.get_species("DagHyd")   # Deep Ones
+  model = species.get_demographic_model("InnsmouthDecline_1M27")
+  contig = species.get_contig(length=10_000)
+  engine = stdvoidsim.get_default_engine()
+  ts = engine.simulate(model, contig, {"DeepOnes": 4})
+  print(ts.num_trees, ts.num_sites)
+
+Use (CLI):
+  stdvoidsim DagHyd -d InnsmouthDecline_1M27 -L 10000 -o out.trees DeepOnes:4
+
+Run the test script (from repo root, after install):
+  python .test/run_simulation.py
+  # or: .test/install_and_run.sh
+
+Run SLiM engine test (script generation + optional run; diploid species only):
+  python .test/run_slim_test.py
+  # Script generation works without SLiM. Actual run requires SLiM on PATH (SLiM 3.x recommended; 4.x may need engine updates).

stdferdowsim-0.1.0/.test/install_and_run.sh

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+#!/usr/bin/env bash
+# From repo root: create venv, install stdgrimmsim, then run the test script.
+set -e
+cd "$(dirname "$0")/.."
+TESTDIR=".test"
+if [ ! -d "$TESTDIR/venv" ]; then
+  echo "Creating venv in $TESTDIR/venv ..."
+  python3 -m venv "$TESTDIR/venv"
+fi
+echo "Activating venv and installing stdgrimmsim (editable)..."
+source "$TESTDIR/venv/bin/activate"
+pip install -e . -q
+echo "Running simulation test..."
+python "$TESTDIR/run_simulation.py"
+deactivate 2>/dev/null || true

stdferdowsim-0.1.0/.test/run_cli_test.sh

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+#!/usr/bin/env bash
+# Run stdgrimmsim CLI (requires venv: run install_and_run.sh first, or have stdgrimmsim on PATH).
+set -e
+cd "$(dirname "$0")/.."
+if [ -d ".test/venv" ]; then
+  source .test/venv/bin/activate
+fi
+stdgrimmsim DagHyd -d InnsmouthDecline_1M27 -L 5000 -o .test/out.trees DeepOnes:4
+echo "Wrote .test/out.trees"
+python3 -c "import tskit; ts=tskit.load('.test/out.trees'); print('  Trees:', ts.num_trees, 'Sites:', ts.num_sites)"
+rm -f .test/out.trees

stdferdowsim-0.1.0/.test/run_simulation.py

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+#!/usr/bin/env python3
+"""Quick test: load stdferdowsim and run tiny simulations for several models."""
+import sys
+from pathlib import Path
+
+# Allow running from repo root without installing (add parent to path)
+repo = Path(__file__).resolve().parent.parent
+if str(repo) not in sys.path:
+    sys.path.insert(0, str(repo))
+
+
+def run_one(engine, species_id, model_id, samples, length=5000, seed=42):
+    import stdferdowsim
+    species = stdferdowsim.get_species(species_id)
+    model = species.get_demographic_model(model_id)
+    contig = species.get_contig(length=length)
+    ts = engine.simulate(model, contig, samples, seed=seed)
+    return ts
+
+
+def main():
+    import stdferdowsim
+
+    engine = stdferdowsim.get_default_engine()
+    tests = [
+        ("ZweBerg", "BlackForest_1D12", {"BlackForest": 4}, "Mountain Dwarves"),
+        ("ZweBerg", "HarzBlackForest_2D12", {"BlackForest": 2, "Harz": 2}, "Dwarves two-pop"),
+        ("NixRhe", "Rhine_1D12", {"Rhine": 4}, "Nix (Rhine)"),
+        ("FraHol", "WellRealm_1D12", {"WellRealm": 4}, "Frau Holle"),
+        ("SchWar", "BlackForest_1D12", {"NorthBlackForest": 4}, "Black Forest spirit"),
+    ]
+
+    for species_id, model_id, samples, label in tests:
+        print(f"{label} ({species_id} / {model_id})")
+        try:
+            ts = run_one(engine, species_id, model_id, samples)
+            print(f"  Trees: {ts.num_trees}, Sites: {ts.num_sites}, Samples: {ts.num_samples}")
+        except Exception as e:
+            print(f"  FAIL: {e}")
+    print("Done")
+
+if __name__ == "__main__":
+    main()