vibepaper 0.1.0__tar.gz

vibepaper-0.1.0/.gitignore

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vibepaper-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 ACRF Cancer Genomics Facility
+
+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.

vibepaper-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: vibepaper
+Version: 0.1.0
+Summary: Data-bound Markdown-to-Word builder for scientific papers
+Project-URL: Repository, https://github.com/PLACEHOLDER/vibepaper
+License: MIT
+License-File: LICENSE
+Keywords: jinja2,manuscript,markdown,pandoc,paper,reproducible-research,scientific-writing
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Text Processing :: General
+Classifier: Topic :: Text Processing :: Markup :: Markdown
+Requires-Python: >=3.10
+Requires-Dist: jinja2>=3.0
+Requires-Dist: lxml>=4.0
+Requires-Dist: pandas>=1.3
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: tomli>=2.0; python_version < '3.11'
+Description-Content-Type: text/markdown
+
+# vibepaper
+
+Build scientific papers from Markdown where every number traces back to the analysis that produced it.
+
+## The problem
+
+Numbers in scientific prose go stale. You finish the analysis, write up the results, and six months later a reviewer asks you to rerun with a corrected dataset. Now you have updated CSVs and a paper full of hardcoded figures: "the mean increased from 4.6 to 9.2", "of the 7,318 variants that lost HIGH impact". Finding every number, checking which is still current, updating without introducing new errors — this is tedious, error-prone, and nearly impossible to review.
+
+## The solution
+
+vibepaper separates computation from communication. Analysis scripts write their key results to named CSV files. The paper references those values by name using Jinja2 template syntax. The build pipeline substitutes every reference before passing the document to pandoc for final Word output.
+
+```markdown
+Mean transcripts per variant doubled from
+{{ vep_impact.giab_mean_v112 | dp(1) }} to
+{{ vep_impact.giab_mean_v115_full | dp(1) }} on upgrading to Ensembl v115.
+```
+
+When you rerun the analysis, you rerun the build. The numbers update everywhere, simultaneously, with a loud error if any reference is missing.
+
+**Three design principles:**
+
+1. **Templates express intent; scripts express computation.** No arithmetic in templates. If you need a percentage increase, the analysis script computes and writes it. The template formats it.
+2. **Loud failures over silent omissions.** A missing or renamed CSV column is a build error, not an empty string in the output.
+3. **Every number is traceable.** Any figure in the rendered paper can be grepped back to the template reference and the script that wrote the CSV.
+
+---
+
+## Installation
+
+```bash
+pip install vibepaper
+```
+
+Requires [pandoc](https://pandoc.org/installing.html) as a system dependency:
+
+```bash
+# macOS
+brew install pandoc
+
+# Debian/Ubuntu
+sudo apt-get install pandoc
+```
+
+---
+
+## Quick start
+
+### Option 1 — paper.toml (recommended for full papers)
+
+Create `paper.toml` in your project root:
+
+```toml
+[paper]
+sections = [
+    "paper/abstract.md",
+    "paper/introduction.md",
+    "paper/methods.md",
+    "paper/results.md",
+    "paper/discussion.md",
+    "paper/references.md",
+    "paper/figures.md",
+]
+supplementary = ["paper/supplementary.md"]
+name = "my_paper"
+```
+
+Then build:
+
+```bash
+vibepaper
+# outputs: output/my_paper_2025-06-01.docx
+#          output/my_paper_supplementary_2025-06-01.docx
+```
+
+### Option 2 — sections file
+
+Create a plain text file listing your sections in order:
+
+```
+# order.txt
+paper/abstract.md
+paper/methods.md
+paper/results.md
+paper/discussion.md
+```
+
+Then:
+
+```bash
+vibepaper --sections-file order.txt --name my_paper
+```
+
+Lines starting with `#` and blank lines are ignored. Paths are relative to the sections file's location.
+
+### Option 3 — direct file list
+
+```bash
+vibepaper paper/abstract.md paper/results.md paper/discussion.md --name my_paper
+```
+
+---
+
+## Template syntax
+
+vibepaper uses [Jinja2](https://jinja.palletsprojects.com/) for template substitution. References follow the pattern `{{ namespace.field | filter }}`.
+
+### Number formatting filters
+
+| Filter | Example | Output |
+|---|---|---|
+| `\| commas` | `{{ n \| commas }}` | `254,129` |
+| `\| dp(n)` | `{{ mean \| dp(1) }}` | `9.2` |
+| `\| pct(n)` | `{{ rate \| pct(1) }}` | `52.2%` |
+| `\| fold(n)` | `{{ ratio \| fold(1) }}` | `2.0-fold` |
+| `\| fmt(spec)` | `{{ v \| fmt('+.1f') }}` | `+3.7` |
+
+`dp` (decimal places) is for numbers that will have surrounding text (e.g. "mean TPV was 9.2"). `pct` appends the `%` sign. Use `fmt` for any format string Python's `format()` accepts.
+
+### Examples
+
+```markdown
+Of {{ clinvar.total_variants | commas }} ClinVar variants, {{ clinvar.gained_high_count | commas }}
+({{ clinvar.gained_high_pct | dp(2) }}%) gained HIGH impact on upgrading to v115.
+
+Mean transcripts per variant increased {{ vep.mean_fold | fold }} from
+{{ vep.mean_v112 | dp(1) }} to {{ vep.mean_v115 | dp(1) }}.
+```
+
+---
+
+## Data sources
+
+### Facts CSVs (primary)
+
+The main data binding mechanism. Analysis scripts write **1-row CSVs** to `output/facts/`. The filename stem becomes the template namespace; column names become field names.
+
+```
+output/facts/
+    transcript_growth.csv      → {{ transcript_growth.v112_count | commas }}
+    vep_impact.csv             → {{ vep_impact.giab_mean_v115_full | dp(1) }}
+    clinvar_reclassification.csv → {{ clinvar_reclassification.total_variants | commas }}
+```
+
+A CSV named `transcript_growth.csv` with columns `v112_count, v115_count`:
+
+```csv
+v112_count,v115_count
+254129,509650
+```
+
+Is referenced as:
+
+```markdown
+Transcripts grew from {{ transcript_growth.v112_count | commas }}
+to {{ transcript_growth.v115_count | commas }}.
+```
+
+vibepaper raises a hard error if a referenced column doesn't exist. It warns if the rendered output contains literal `nan`, `None`, or unresolved `{{`.
+
+### JSON data (supplemental)
+
+Pass additional values directly without creating a CSV file:
+
+```bash
+# Inline dict
+vibepaper --data '{"cohort_size": 412, "stats": {"pvalue": 0.003}}'
+
+# From file
+vibepaper --data results.json
+```
+
+Top-level keys become namespaces:
+
+```markdown
+Cohort: {{ cohort_size }} participants (p = {{ stats.pvalue | dp(3) }}).
+```
+
+JSON is merged on top of facts CSVs. Nested dicts are deep-merged at the namespace level; scalar values override directly.
+
+---
+
+## Table directives
+
+For supplementary tables, embed CSVs directly into the Markdown with a directive comment:
+
+```markdown
+<!-- include-csv: output/consequence_changes.csv
+  columns: [consequence, v112_count, v115_count, pct_change]
+  rename:
+    v112_count: v112
+    v115_count: v115
+    pct_change: Change (%)
+  format:
+    v112_count: ",d"
+    v115_count: ",d"
+    pct_change: ".1f"
+  sort: [-pct_change]
+  max_rows: 20
+-->
+```
+
+Directive options:
+
+| Option | Description |
+|---|---|
+| `columns` | List of columns to include, in order |
+| `rename` | Dict mapping column names to display names |
+| `format` | Dict mapping column names to Python format specs |
+| `align` | `left`, `right`, `center`, or per-column dict |
+| `sort` | List of column names; prefix `-` for descending |
+| `filter` | pandas `query()` expression |
+| `max_rows` | Truncate to this many rows |
+| `na_rep` | String to use for missing values (default: `—`) |
+
+---
+
+## paper.toml reference
+
+```toml
+[paper]
+# Manuscript sections in order (paths relative to paper.toml)
+sections = [
+    "paper/title.md",
+    "paper/abstract.md",
+    "paper/introduction.md",
+    "paper/methods.md",
+    "paper/results.md",
+    "paper/discussion.md",
+    "paper/references.md",
+    "paper/figures.md",
+]
+
+# Built as a separate .docx unless --combined is passed
+supplementary = ["paper/supplementary.md"]
+
+# Output filename stem: {name}_{date}.docx
+# Default: parent directory name
+name = "my_paper"
+
+# Directory of 1-row facts CSVs
+# Default: "output/facts"
+facts_dir = "output/facts"
+
+# Output directory for .docx files
+# Default: "output"
+output_dir = "output"
+
+# Intermediate build directory
+# Default: "build"
+build_dir = "build"
+
+# Word reference document for custom formatting (double spacing, line numbers, etc.)
+# Only used if the file exists; silently skipped otherwise.
+# Default: "paper/reference.docx"
+reference_doc = "paper/reference.docx"
+```
+
+### Word reference document
+
+To apply journal-specific formatting (e.g. double line spacing, continuous line numbering):
+
+1. Open a blank Word document
+2. Set paragraph spacing to Double and enable Layout → Line Numbers → Continuous
+3. Save as `paper/reference.docx`
+
+vibepaper will use it automatically if it exists at the configured path.
+
+---
+
+## CLI reference
+
+```
+vibepaper [FILE.md ...] [options]
+
+Input (choose one):
+  FILE.md ...           Markdown files in order (no paper.toml needed)
+  --sections-file FILE  Plain text file with one .md path per line
+  --config FILE         paper.toml config file (default: paper.toml)
+
+Data:
+  --data JSON           JSON file path or inline dict for template context
+  --facts-dir DIR       Override facts CSV directory
+
+Output:
+  --output-dir DIR      Output directory for .docx files
+  --name NAME           Output filename stem
+  --combined            Merge supplementary into main document
+```
+
+---
+
+## Project layout convention
+
+```
+my_paper/
+├── paper.toml
+├── paper/
+│   ├── abstract.md
+│   ├── introduction.md
+│   ├── methods.md
+│   ├── results.md
+│   ├── discussion.md
+│   ├── references.md
+│   ├── figures.md
+│   ├── supplementary.md
+│   └── reference.docx        ← optional Word formatting template
+├── output/
+│   ├── facts/
+│   │   ├── cohort.csv        ← 1-row: n_patients, n_controls, ...
+│   │   ├── model_results.csv ← 1-row: auc, pvalue, effect_size, ...
+│   │   └── ...
+│   └── tables/
+│       └── full_results.csv  ← multi-row: used in include-csv directives
+└── scripts/
+    └── run_analysis.py       ← writes to output/facts/
+```