init-python-project

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Initialize Python Project (New or Fork). Use when the user wants to create a new production-ready Python/ML project structure, or fork and enhance an existing project. Uses uv for environment management.

14installs

Sourcea-green-hand-jack/ml-research-skills

Added on2026-05-02

NPX Install

npx skill4agent add a-green-hand-jack/ml-research-skills init-python-project

SKILL.md Content

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Initialize Python Project

Help the user create a production-ready Python project or upgrade an existing one without inlining large file bodies inside this skill. Use the bundled references and templates as the source of truth.

Skill Directory Layout

text

<installed-skill-dir>/
├── SKILL.md
├── references/
│   ├── architecture.md
│   ├── new-project.md
│   ├── fork-enhancement.md
│   └── best-practices.md
├── scripts/
│   └── scaffold_new_project.py
├── template_manifest.json
└── templates/
    ├── common/
    │   ├── .gitignore
    │   ├── .env.example
    │   ├── README.md
    │   ├── CLAUDE.md
    │   ├── pyproject.toml.tmpl
    │   ├── tests/
    │   └── docs/
    └── ml/
        ├── .agent/
        ├── docs/
        ├── experiments/
        ├── infra/
        ├── eval/
        └── scripts/

Progressive Loading

Read only the references needed for the current path:

Always read
```
references/architecture.md
```
For new projects, read
```
references/new-project.md
```
For fork/enhancement work, read
```
references/fork-enhancement.md
```
If you need policy, tradeoff, or failure-handling guidance, read
```
references/best-practices.md
```

Use

templates/

as the source of truth for file contents instead of reproducing long inline snippets. Use

template_manifest.json

as the source of truth for which template groups and placeholders the scaffold supports.

Step 1 — Gather Project Information

Ask the user in a single message:

Project type:
- ```
new
```
  — create a new project
- ```
fork
```
  — clone and enhance an existing repository
If
```
new
```
:
- Project name
- Package name (default: snake_case of project name)
- Short description
- Python version (default:
```
3.11
```
  )
- Project type:
```
ml
```
  ,
```
web
```
  ,
```
lib
```
  , or
```
general
```
If
```
fork
```
:
- GitHub repository URL
- Whether they want a fork workflow or just a local enhancement
For both:
- GitHub repository URL for the target repo, if available
- Author name and email

Wait for the answer before continuing.

Step 2 — Choose the Execution Path

Path A: New Project

Read

references/new-project.md

and

references/architecture.md

2A.1 Create the project root

bash

mkdir <project-name>
cd <project-name>
uv init --name <package_name> --python <version>

If the directory already exists, stop and ask whether to choose a new name or reuse it.

2A.2 Preferred path for

new + ml

For a new ML project, prefer the bundled scaffold script:

bash

python3 <installed-skill-dir>/scripts/scaffold_new_project.py \
  <target-dir> \
  --project-name <project-name> \
  --package-name <package-name> \
  --description "<short-description>" \
  --python-version <version> \
  --author-name "<author-name>" \
  --author-email "<author-email>" \
  --repo-url "<repo-url-or-TBD>"

The script handles:

```
uv init
```
source/test/docs directory creation
copying templates from
```
templates/common/
```
and
```
templates/ml/
```
placeholder replacement
creating
```
.env
```
bootstrapping remote-project memory files for local-to-remote workflows
writing
```
.gitkeep
```
files

After it completes, continue with install, verification, and git setup in Steps 2A.6 and 2A.7.

If the user wants a non-ML layout or the script is not suitable, fall back to the manual path below.

2A.3 Manual fallback: create the directory layout

For

ml

projects, create the full four-layer structure from

references/architecture.md

At minimum, create:

bash

mkdir -p src/<package_name>/{models,data,utils}
mkdir -p tests/{data,outputs}
mkdir -p docs/outlines docs/dev/features docs/src docs/results docs/reports docs/runs
mkdir -p .vscode .cursor .claude/commands
touch src/<package_name>/__init__.py
touch src/<package_name>/models/__init__.py
touch src/<package_name>/data/__init__.py
touch src/<package_name>/utils/__init__.py
touch tests/__init__.py

For non-ML projects, keep the common project files but only create ML-specific directories if the user explicitly wants them.

2A.4 Materialize templates

Use the templates under

templates/

and replace placeholders:

```
{{PROJECT_NAME}}
```
```
{{PACKAGE_NAME}}
```
```
{{DESCRIPTION}}
```
```
{{PYTHON_VERSION}}
```
```
{{AUTHOR_NAME}}
```
```
{{AUTHOR_EMAIL}}
```
```
{{REPO_URL}}
```

Write these common files from

templates/common/

```
.gitignore
```
```
.env.example
```
```
README.md
```
```
CLAUDE.md
```
```
pyproject.toml
```
```
tests/conftest.py
```
```
docs/outlines/project_plan.md
```
```
docs/outlines/progress.md
```
```
docs/results/.gitkeep
```
```
docs/reports/.gitkeep
```
```
docs/runs/.gitkeep
```
```
docs/dev/feature_template.md
```
```
docs/src/dependencies.md
```
```
.vscode/settings.json
```

For

ml

projects, also write:

```
experiments/config.py
```
```
experiments/configs/base.yaml
```
```
infra/envs/local.yaml
```
```
infra/envs/cluster.yaml.example
```
```
infra/remote-projects.yaml
```
```
infra/README.md
```
```
docs/ops/current-status.md
```
```
docs/ops/decision-log.md
```
```
.agent/local-overrides.yaml
```
```
eval/baselines/README.md
```
```
scripts/train.py
```
```
scripts/download_data.py
```

Create

.env

as an empty file with a short comment header if it does not exist.

2A.5 Add placeholder files for empty directories

Use

.gitkeep

where needed so empty directories are tracked:

bash

touch experiments/configs/.gitkeep
touch eval/benchmarks/.gitkeep
touch eval/baselines/reproduced/.gitkeep
touch infra/submit/slurm/.gitkeep
touch docs/results/.gitkeep
touch docs/reports/.gitkeep
touch docs/runs/.gitkeep
touch tests/data/.gitkeep
touch tests/outputs/.gitkeep

Only create placeholders for directories that actually exist in the chosen project type.

2A.6 Install and verify

For ML projects:

bash

uv pip install -e ".[dev,ml]"

For non-ML projects:

bash

uv pip install -e ".[dev]"

Run an initial test:

bash

pytest tests/ -v

If there are no tests yet, create a placeholder test and rerun:

bash

cat > tests/test_placeholder.py <<'EOF'
def test_placeholder():
    assert True
EOF
pytest tests/

2A.7 Initialize git and optional remote

bash

git rev-parse --git-dir >/dev/null 2>&1 || git init
git add .
git commit -m "Initial Python project structure"

If the user provided a GitHub URL, add

origin

, show

git remote -v

, and ask before pushing:

bash

git remote add origin <github-ssh-url>
CURRENT_BRANCH="$(git branch --show-current)"
git push -u origin "$CURRENT_BRANCH"

Path B: Fork / Existing Project

Read

references/fork-enhancement.md

references/architecture.md

, and

references/best-practices.md

2B.1 Clone and inspect

bash

git clone <github-ssh-url> <project-name>
cd <project-name>
ls -la

Check for:

```
pyproject.toml
```
,
```
setup.py
```
,
```
requirements.txt
```
```
src/
```
,
```
tests/
```
,
```
docs/
```
,
```
scripts/
```

.env.example

CLAUDE.md

.vscode/settings.json

2B.2 Report gaps before bulk edits

Produce a concise report showing:

Existing structure
Missing high-value components
Whether the repo is already installable
Whether docs/test isolation are missing

Then ask whether to:

Add all missing components
Add only selected components
Generate a checklist without editing

2B.3 Add only missing components

When the user approves edits, use the templates under

templates/common/

to fill gaps:

```
.env.example
```
```
CLAUDE.md
```
```
tests/conftest.py
```
docs templates
```
.vscode/settings.json
```
```
pyproject.toml
```
if migrating from
```
requirements.txt
```

Do not force the full ML layout onto an existing repo unless the user explicitly wants that migration.

Template Application Rules

Keep existing substantial files when they are already good enough.
Prefer surgical edits over overwriting.
For templated files, replace placeholders consistently.
If a template is only partially relevant, copy the relevant sections instead of dumping the whole file verbatim.

Final Summary

Report:

text

✓ Python project initialized or enhanced: <project-name>
✓ Project type: <new|fork> / <ml|web|lib|general>
✓ Common scaffolding applied
✓ UV environment configured
✓ Git status: initialized / existing repo reused
✓ Remote: <configured or skipped>

Project location: <full-path>

Next steps:
1. cd <project-name>
2. cp .env.example .env
3. Fill in project-specific settings
4. Start implementing in src/<package_name>/
5. Put stable experiment summaries in docs/results/, reports in docs/reports/, and run pointers in docs/runs/
6. Run pytest before the next commit

Important Notes

Use
```
references/best-practices.md
```
when you hit edge cases.
Keep this
```
SKILL.md
```
focused on orchestration; the detailed file content should live in
```
templates/
```
and
```
references/
```
.
```
experiments/
```
is runnable experiment logic, not a result archive. Raw outputs, checkpoints, logs, and wandb/tensorboard caches should stay in ignored paths or external storage, with small pointers in
```
docs/runs/
```
.
When this code repo belongs to a project control root, prefer sibling code worktrees under
```
<ProjectName>/code-worktrees/
```
instead of nested worktrees inside
```
code/
```
.

init-python-project

NPX Install

Tags

SKILL.md Content

Initialize Python Project

Skill Directory Layout

Progressive Loading

Step 1 — Gather Project Information

Step 2 — Choose the Execution Path

Path A: New Project

2A.1 Create the project root

2A.2 Preferred path for
`new + ml`

2A.3 Manual fallback: create the directory layout

2A.4 Materialize templates

2A.5 Add placeholder files for empty directories

2A.6 Install and verify

2A.7 Initialize git and optional remote

Path B: Fork / Existing Project

2B.1 Clone and inspect

2B.2 Report gaps before bulk edits

2B.3 Add only missing components

Template Application Rules

Final Summary

Important Notes