capscorp 0.1.0__tar.gz

capscorp-0.1.0/.claude/launch.json

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+{
+  "version": "0.0.1",
+  "configurations": [
+    {
+      "name": "docs",
+      "runtimeExecutable": "pixi",
+      "runtimeArgs": [
+        "run",
+        "-e",
+        "docs",
+        "mkdocs",
+        "serve",
+        "-a",
+        "127.0.0.1:8123"
+      ],
+      "port": 8123
+    }
+  ]
+}

capscorp-0.1.0/.gitattributes

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+# SCM syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true

capscorp-0.1.0/.github/workflows/ci.yml

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+name: ci
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+concurrency:
+  group: ci-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: prefix-dev/setup-pixi@v0.8.1
+        with:
+          environments: default
+          cache: true
+
+      - name: Install the package
+        run: pixi run postinstall
+
+      - name: Lint
+        run: pixi run pre-commit-run
+
+      - name: Typecheck
+        run: pixi run typecheck
+
+      # Integration tests are excluded by default: they call a real model and cost
+      # money. Run them locally with `pixi run test-integration`.
+      - name: Test
+        run: pixi run test
+
+      - name: Build docs
+        run: pixi run docs-build

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

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+name: docs
+
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Never cancel a deploy midway; let an in-flight one finish.
+concurrency:
+  group: pages
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: prefix-dev/setup-pixi@v0.8.1
+        with:
+          environments: docs
+          cache: true
+
+      - name: Build site
+        run: pixi run -e docs docs-build
+
+      - uses: actions/upload-pages-artifact@v3
+        with:
+          path: site
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - id: deployment
+        uses: actions/deploy-pages@v4

capscorp-0.1.0/.github/workflows/release.yaml

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+name: release
+
+on:
+  push:
+    tags: ["v*"]
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: astral-sh/setup-uv@v5
+
+      # A tag that disagrees with the packaged version would publish something
+      # nobody can correlate with the repo.
+      - name: Check the tag matches the packaged version
+        if: startsWith(github.ref, 'refs/tags/')
+        run: |
+          tag="${GITHUB_REF_NAME#v}"
+          pkg="$(grep -m1 '^version = ' pyproject.toml | cut -d'"' -f2)"
+          if [ "$tag" != "$pkg" ]; then
+            echo "tag v$tag does not match pyproject version $pkg" >&2
+            exit 1
+          fi
+          echo "releasing $pkg"
+
+      - name: Build sdist and wheel
+        run: uv build
+
+      - name: Check the artifacts
+        run: uvx twine check dist/*
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/capscorp
+    permissions:
+      # Required for PyPI trusted publishing. No API token is stored anywhere.
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - uses: pypa/gh-action-pypi-publish@release/v1

capscorp-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#   Usually these files are written by a python script from a template
+#   before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+# Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+# uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+# poetry.lock
+# poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+# pdm.lock
+# pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+# pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# Redis
+*.rdb
+*.aof
+*.pid
+
+# RabbitMQ
+mnesia/
+rabbitmq/
+rabbitmq-data/
+
+# ActiveMQ
+activemq-data/
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#   JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#   be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#   and can be added to the global gitignore or merged into this file.  For a more nuclear
+#   option (not recommended) you can uncomment the following to ignore the entire idea folder.
+# .idea/
+
+# Abstra
+#   Abstra is an AI-powered process automation framework.
+#   Ignore directories containing user credentials, local state, and settings.
+#   Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#   Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
+#   that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#   and can be added to the global gitignore or merged into this file. However, if you prefer,
+#   you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+# Temporary file for partial code execution
+tempCodeRunnerFile.py
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Streamlit
+.streamlit/secrets.toml
+
+# pixi
+.pixi/
+*.egg-info/
+
+# capsule-corp local index (rebuildable from files)
+.capsule-corp/index.db
+
+# built docs site
+site/

capscorp-0.1.0/.pre-commit-config.yaml

@@ -0,0 +1,43 @@
+exclude: ^(\.copier-answers\.yml)|.pixi$
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-toml
+
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.3.0
+    hooks:
+      - id: ruff
+        # Block style, not [flow, style]: YAML splits flow sequences on commas, which
+        # would turn --select=C901,E501 into a flag plus a bogus filename.
+        args:
+          - --fix
+          - --select=C901,E501
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.8.0
+    hooks:
+      - id: mypy
+        # The hook runs in its own isolated env, so it needs the runtime
+        # dependencies whose decorators and models appear in our signatures.
+        additional_dependencies:
+          - types-setuptools
+          - pydantic
+          - typer
+          - pytest
+          - tomlkit
+          - platformdirs
+          - rich
+          - textual
+          - mcp
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+        types_or: [yaml, json, markdown, toml]

capscorp-0.1.0/.prettierignore

@@ -0,0 +1,7 @@
+build
+conda.recipe
+.copier-answers.yml
+.pixi
+
+*.html
+*.properties

capscorp-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 lenzpracher
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

capscorp-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: capscorp
+Version: 0.1.0
+Summary: A terminal catalogue of reproducible, pre-registered research capsules
+Author-email: Lenz Pracher <lenz.pracher@gmail.com>
+License: MIT
+Project-URL: Homepage, https://github.com/lenzpracher/capsule-corp
+Project-URL: Repository, https://github.com/lenzpracher/capsule-corp
+Keywords: research,reproducibility,pre-registration,llm,tui
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: typer>=0.12
+Requires-Dist: textual>=0.80
+Requires-Dist: pydantic<3,>=2.7
+Requires-Dist: tomlkit>=0.13
+Requires-Dist: rich>=13
+Requires-Dist: platformdirs>=4
+Requires-Dist: mcp<3,>=2.2
+Dynamic: license-file
+
+<p align="center">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="docs/assets/logo-dark.svg">
+    <img src="docs/assets/logo.svg" alt="capsule" width="440">
+  </picture>
+</p>
+
+# capsule-corp
+
+Packaging reproducible research questions.
+
+A terminal catalogue where each **capsule** is one empirically testable research question,
+packaged so that it stays reproducible and honest: the question, a frozen pre-registration,
+the code, a pinned environment, the outputs, and a verification record.
+
+Capsules are primarily written by an LLM. Every artifact is plain text and editable by hand.
+
+## Why pre-registration
+
+The failure mode of LLM-generated research is not bad code — it is code that quietly gets
+rewritten until it agrees with the conclusion. capsule-corp splits a capsule into two phases
+with a lock in between:
+
+1. **Design.** An agent writes the question, the hypothesis, and a set of _machine-checkable_
+   assertions that would falsify it — before any implementation exists.
+2. **Freeze.** `prereg.toml` is hashed into `.prereg.lock` and committed. From here the
+   predictions and the checks cannot change.
+3. **Implement, run, verify.** A second agent writes the code. The hash is re-verified before
+   and after; if the pre-registration moved, the run fails.
+
+Verification then has two independent layers: the deterministic checks (no LLM involved, so
+they are a real gate), and a **blinded** LLM judge that sees the question, the code, and the
+outputs — but not the write-up or any of the author's claims.
+
+A capsule whose hypothesis is refuted is a _successful_ capsule. That outcome is recorded,
+not treated as a failure.
+
+## Status
+
+Early but complete end to end: catalogue, agent loop, pre-registered verification, TUI,
+remote execution, and the MCP server are all implemented. The Slurm, SSH and Modal
+backends are unit-tested but have not yet been pointed at real infrastructure — see
+[`docs/roadmap.md`](docs/roadmap.md).
+
+## Install
+
+```bash
+curl -fsSL https://lenzpracher.github.io/capsule-corp/install.sh | sh
+```
+
+This puts the `capsule` command in `~/.local/bin` using [uv](https://docs.astral.sh/uv/),
+in its own isolated environment. No sudo. As with any installer of this shape, read
+[the script](install.sh) before piping it to a shell.
+
+Or, equivalently:
+
+```bash
+uv tool install capscorp
+```
+
+The command is `capsule`; the package is `capscorp` and the repository is
+`capsule-corp`. Only the first is something you type.
+
+To hack on capsule-corp itself, clone it and install editable so the command tracks
+your working copy:
+
+```bash
+git clone https://github.com/lenzpracher/capsule-corp
+cd capsule-corp
+uv tool install --editable .
+pixi install && pixi run postinstall   # for the test and lint tasks
+```
+
+Then run `capsule doctor`. Two external tools do the real work:
+[pi](https://github.com/earendil-works/pi) writes the capsules, and
+[pixi](https://pixi.sh) manages each capsule's environment.
+
+## Use
+
+```bash
+capsule doctor                   # check pi, pixi and the compute backends
+capsule init ~/research          # create a catalogue
+capsule mkdir optimization       # organise it however you like
+
+capsule new "Does LR warmup lower final loss?" --folder optimization
+capsule design 0001              # write the pre-registration; re-run to revise it
+capsule freeze 0001              # lock it; predictions can no longer change
+capsule implement 0001           # write the code
+capsule run 0001 --on slurm      # local (default), slurm, ssh, or modal
+capsule verify 0001              # checks, then the blinded judge
+
+capsule open 0001                # read the code in VS Code
+capsule export 0001              # a supplementary-materials bundle for a paper
+capsule tui                      # browse and drive it interactively
+capsule mcp                      # serve the catalogue to any MCP client
+capsule search warmup
+```
+
+Commands are listed in `capsule --help` in the order you run them, grouped by purpose,
+because that sequence is the method rather than an implementation detail.
+
+## Interface
+
+`capsule tui` opens a Textual interface over the same library the CLI uses: a folder
+tree, a detail pane showing the pre-registration and the verdict, a settings view, and
+`r`un / `v`erify / `d`esign / `f`reeze / `i`mplement keybinds. Press `e` for a built-in
+file browser and editor with syntax highlighting, or `o` to open the capsule in
+VS Code. Phases run in worker threads, so the interface stays responsive while a model
+is working.
+
+Long phases stream their progress as they run — each file the agent writes, each
+command it runs, a live token count — so you can tell a working agent from a hung one.
+
+## Attaching capsules to papers
+
+```bash
+capsule export 0001                     # supplementary-materials zip
+capsule export 0001 --format markdown   # an appendix
+capsule export 0001 --format html       # one self-contained file
+```
+
+Every export carries the pre-registration hash and the provenance, and discloses any
+revision the registration went through after being frozen. See
+[`docs/export.md`](docs/export.md).
+
+## Running elsewhere
+
+Capsules run locally by default, and unchanged on Slurm, any SSH host with Docker, or
+Modal. See [`docs/compute.md`](docs/compute.md).
+
+## Driving it from an MCP client
+
+`capsule mcp` serves the catalogue over the Model Context Protocol, including
+`capsule://<id>` resources so an agent can read prior capsules as context. See
+[`docs/mcp.md`](docs/mcp.md).
+
+## A capsule on disk
+
+```
+capsules/optimization/0001-lr-warmup/
+  capsule.toml         manifest: id, status, provenance
+  QUESTION.md          the research question
+  prereg.toml          hypothesis, predictions, checks
+  .prereg.lock         sha256 of prereg.toml at freeze time
+  AGENTS.md            instructions for the implementing agent
+  .pi/settings.json    per-capsule pinned agent config
+  pixi.toml            per-capsule environment
+  src/  run.py         the implementation
+  results/             results.json + figures/
+  runs/<timestamp>/    transcript and provenance for each run
+  verification.json    check results + judge verdict
+  REPORT.md            the write-up
+```
+
+Files are the source of truth. The SQLite index is a cache and can be rebuilt at any time
+with `capsule reindex`.
+
+## Agent independence
+
+The coding agent is [`pi`](https://github.com/earendil-works/pi), which is open source and
+provider-agnostic — configure it for Claude, GPT, Gemini, or a local model. capsule-corp does
+not pin a model; it inherits whatever `pi` is configured with and records what was actually
+used in each capsule's manifest. The runner sits behind a protocol, so other agents can be
+plugged in.
+
+## Documentation
+
+<https://lenzpracher.github.io/capsule-corp>
+
+## License
+
+MIT
+
+## Disclaimer
+
+capsule-corp is an independent, unaffiliated open-source project. It is not
+associated with, endorsed by, or sponsored by Bird Studio, Shueisha, Toei Animation,
+or Capsule Corporation Tokyo. "Dragon Ball" and "Capsule Corporation" are trademarks
+of their respective owners; the name and mark here are an affectionate nod, and no
+rights-holder artwork is used.