Progress

pyproject.toml

@@ -64,6 +64,7 @@ scipy = [
     { version = ">=1.10.0,<=1.10.1", python = "<3.9" },
     { version = ">=1.10.0", python = ">=3.9" }
 ]
+copier = "^8.1.0"
 
 [tool.poetry.group.dev.dependencies]
 black = "^23.1.0"

snakebids/project_template/copier.yaml

@@ -0,0 +1,45 @@
+full_name:
+  type: str
+  help: What is your name?
+  placeholder: " optional"
+
+email:
+  type: str
+  help: What is your email?
+
+github:
+  type: str
+  help: What is your github username?
+
+app_full_name:
+  type: str
+  help: What is the name of your app?
+  default: "{{ dst_path }}"
+  validator: '{% if not app_full_name %}Required{% endif %}'
+
+app_description:
+  type: str
+  help: Provide a brief description of your app
+
+app_version:
+  default: "0.1.0"
+  help: Starting version number for your app
+
+create_doc_template:
+  type: bool
+  help: Would you to set up basic documentation?
+
+bids_version:
+  default: "1.8.0"
+  when: false
+
+snakebids_version:
+  default: "0.0.0"
+  when: false
+
+name_slug:
+  default: "{{ app_full_name|lower|replace(' ', '_')|replace('-', '_') }}"
+  when: false
+
+_jinja_extensions:
+  - jinja2_time.TimeExtension

snakebids/project_template/{{ name_slug }}/README.md.jinja

@@ -0,0 +1,3 @@
+# {{app_full_name}}
+
+{{ app_description }}

snakebids/project_template/{{cookiecutter.__app_name}}/setup.py → snakebids/project_template/{{ name_slug }}/setup.py.jinja

@@ -34,11 +34,11 @@
     ],
     entry_points={
         "console_scripts": [
-            "{{cookiecutter.__app_name}}={{cookiecutter.__app_name}}.run:main"
+            "{{name_slug}}={{name_slug}}.run:main"
         ]
     },
     install_requires=[
-        "snakebids>={{cookiecutter._snakebids_version}}",
+        "snakebids>={{snakebids_version}}",
         "snakemake",
     ],
     python_requires=">=3.7",

snakebids/project_template/{{cookiecutter.__app_name}}/docs/conf.py → snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/conf.py.jinja

@@ -17,9 +17,9 @@
 # -- Project information -----------------------------------------------------
 
 
-project = "{{cookiecutter.__app_name}}"
-copyright = "{% now 'utc', '%Y' %}, {{cookiecutter.full_name}}"
-author = "{{cookiecutter.full_name}}"
+project = "{{name_slug}}"
+copyright = "{% now 'utc', '%Y' %}, {{full_name}}"
+author = "{{full_name}}"
 
 
 # -- General configuration ---------------------------------------------------

snakebids/project_template/{{cookiecutter.__app_name}}/docs/getting_started/installation.md → snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/getting_started/installation.md.jinja

@@ -3,7 +3,7 @@
 Install from github with pip:
 
 ```bash
-pip install -e git+https://github.com/{{cookiecutter.github}}/{{cookiecutter.__app_name}}#egg={{cookiecutter.__app_name}}
+pip install -e git+https://github.com/{{github}}/{{name_slug}}#egg={{name_slug}}
 ```
 
 Note: you can re-run this command to re-install with the latest version
@@ -13,13 +13,13 @@ Note: you can re-run this command to re-install with the latest version
 Do a dry-run first (`-n`) and simply print (`-p`) what would be run:
 
 ```bash
-{{cookiecutter.__app_name}} /path/to/bids/dir /path/to/output/dir participant -np
+{{name_slug}} /path/to/bids/dir /path/to/output/dir participant -np
 ```
 
 Run the app, using all cores::
 
 ```bash
-{{cookiecutter.__app_name}} /path/to/bids/dir /path/to/output/dir participant --cores all
+{{name_slug}} /path/to/bids/dir /path/to/output/dir participant --cores all
 ```
 
 If any workflow rules require containers, then run with the `--use-singularity` option.
@@ -35,22 +35,22 @@ summarize outputs, by using the `report(...)` function on any snakemake output.
 To generate a report, run:
 
 ```bash
-{{cookiecutter.__app_name}} /path/to/bids/dir /path/to/output/dir participant --report
+{{name_slug}} /path/to/bids/dir /path/to/output/dir participant --report
 ```
 
 ## Compute Canada Instructions
 
 ### Setting up a dev environment
 
-Here are some instructions to get your python environment set-up on graham to run {{ cookiecutter.__app_name }}:
+Here are some instructions to get your python environment set-up on graham to run {{name_slug}}:
 
 # Create a virtualenv and activate it:
 
 ```bash
 cd $SCRATCH
 module load python/3
-virtualenv venv_{{ cookiecutter.__app_name }}
-source venv_{{ cookiecutter.__app_name }}/bin/activate
+virtualenv venv_{{name_slug}}
+source venv_{{name_slug}}/bin/activate
 ```
 
 # Follow the steps above to install from github repository
@@ -69,23 +69,23 @@ These are used in the instructions below.
 In an interactive job (for testing):
 
 ```bash
-regularInteractive -n 8 {{ cookiecutter.__app_name }} bids_dir out_dir participant --participant_label 001 -j 8
+regularInteractive -n 8 {{name_slug}} bids_dir out_dir participant --participant_label 001 -j 8
 ```
 
 Submitting a job (for larger cores, more subjects), still single job, but snakemake will parallelize over the 32 cores:
 
 ```bash
-regularSubmit -j Fat {{ cookiecutter.__app_name }} bids_dir out_dir participant  -j 32
+regularSubmit -j Fat {{name_slug}} bids_dir out_dir participant  -j 32
 ```
 
 Scaling up to ~hundred subjects (needs cc-slurm snakemake profile installed), submits 1 16core job per subject:
 
 ```bash
-{{ cookiecutter.__app_name }} bids_dir out_dir participant  --profile cc-slurm
+{{name_slug}} bids_dir out_dir participant  --profile cc-slurm
 ```
 
 Scaling up to even more subjects (uses group-components to bundle multiple subjects in each job), 1 32core job for N subjects (e.g. 10):
 
 ```bash
-{{ cookiecutter.__app_name }} bids_dir out_dir participant  --profile cc-slurm --group-components subj=10
-```
+{{name_slug}} bids_dir out_dir participant  --profile cc-slurm --group-components subj=10
+```

snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/requirements.txt.jinja

@@ -0,0 +1,4 @@
+docutils<0.18
+sphinx-argparse
+sphinx_rtd_theme
+snakebids=={{ snakebids_version }}

snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/usage/app_cli.md.jinja

@@ -0,0 +1,7 @@
+## Command line interface
+
+```{argparse}
+:filename: ../{{ name_slug }}/run.py
+:func: get_parser
+:prog: {{ name_slug }}
+```

snakebids/project_template/{{cookiecutter.__app_name}}/docs/usage/snakemake_cli.md → snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/usage/snakemake_cli.md

@@ -4,4 +4,4 @@
 :module: snakemake
 :func: get_argument_parser
 :prog: snakemake
-```
+```

snakebids/project_template/{{cookiecutter.__app_name}}/{{cookiecutter.__app_name}}/config/snakebids.yml → snakebids/project_template/{{ name_slug }}/{{name_slug}}/config/snakebids.yml

@@ -80,7 +80,7 @@ parse_args:
  # below are examples for plugin and custom parameters (e.g. config['smoothing_fwhm'])
   --skip_bids_validation:
     help: 'Skip validation of BIDS dataset. BIDS validation is performed by
-          default using the bids-validator plugin (if installed/enabled) or with the pybids 
+          default using the bids-validator plugin (if installed/enabled) or with the pybids
           validator implementation (if bids-validator is not installed/enabled).'
     dest: "plugins.validator.skip"
     action: "store_true"

snakebids/project_template/{{ name_slug }}/{{name_slug}}/pipeline_description.json.jinja

@@ -0,0 +1,22 @@
+{%
+    set generated = {
+        "Name":  name_slug,
+        "Version": app_version,
+    }
+-%}
+{%- if github -%}
+    {%- set _ = generated.update({"CodeURL": "https://github.com/" + github + "/" + name_slug}) -%}
+{%- endif -%}
+{%- if full_name -%}
+    {%- set _ = generated.update({"Author": full_name}) -%}
+{%- endif -%}
+{%- if email -%}
+    {%- set _ = generated.update({"AuthorEmail": email}) -%}
+{%- endif -%}
+{{- {
+        "Name": "Dataset generated by " + name_slug,
+        "BIDSVersion":  bids_version,
+        "DatasetType": "derivative",
+        "GeneratedBy": [generated],
+    } | to_json(indent=2)
+}}

snakebids/project_template/{{cookiecutter.__app_name}}/{{cookiecutter.__app_name}}/run.py → snakebids/project_template/{{ name_slug }}/{{name_slug}}/run.py.jinja

@@ -7,7 +7,7 @@
 
 def get_parser():
     """Exposes parser for sphinx doc generation, cwd is the docs dir"""
-    app = SnakeBidsApp("../{{ cookiecutter.__app_name }}")
+    app = SnakeBidsApp("../{{ name_slug }}")
     return app.parser