Merge pull request #11 from pharmaverse/setup-project

Set up project structure

Author: nanxstats

.github/workflows/ci-tests.yml

@@ -0,0 +1,56 @@
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+name: CI Tests
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          # we are using the -e flag, so that code cov finds the source.
+          # this is not ideal, since installing an editable can technically
+          # differ from a normal install in surprising ways.
+          pip install -e '.[all]'
+      - name: Test with pytest
+        run: |
+          pip install pytest pytest-cov
+          pytest --cov=rtflite --cov-report=xml
+
+      # - name: Upload coverage reports to Codecov
+      #   uses: codecov/codecov-action@v4
+      #   with:
+      #     name: "py${{ matrix.python-version }}"
+      #     token: ${{ secrets.CODECOV_TOKEN }}
+
+  test-windows:
+    runs-on: windows-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+      - name: Install dependencies
+        run: |
+          pip install -e '.[all]'
+      - name: Test with pytest
+        run: |
+          pip install pytest pytest-cov
+          pytest --cov=rtflite --cov-report=xml

.github/workflows/mkdocs.yml

@@ -0,0 +1,42 @@
+name: mkdocs
+
+on:
+  push:
+    branches:
+      - main
+
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
+
+      - uses: actions/cache@v4
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+
+      - name: Install dependencies
+        run: |
+          pip install mkdocs-material mkdocstrings-python
+          pip install pytest pytest-cov
+          pip install -e '.[all]'
+
+      - name: Generate coverage report and deploy mkdocs site
+        run: |
+          pytest --cov=rtflite --cov-report=html:docs/coverage/
+          mkdocs gh-deploy --force

.gitignore

@@ -0,0 +1,19 @@
+# OS
+.DS_Store
+
+# Python
+__pycache__/
+*.py[oc]
+build/
+dist/
+wheels/
+*.egg-info
+
+# pytest
+.coverage
+
+# venv
+.venv
+
+# r2rtf
+Rplots.pdf

.python-version

@@ -0,0 +1 @@
+3.13.1

CHANGELOG.md

@@ -0,0 +1,8 @@
+# Changelog
+
+## rtflite 0.1.0
+
+### New features
+
+- Add `CHANGELOG.md` to record changes.
+- Add essential metadata to `pyproject.toml`.

LICENSE

@@ -1,21 +1,20 @@
-MIT License
-
 Copyright (c) 2025 pharmaverse
 
-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:
+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 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.
+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.

LICENSES_THIRD_PARTY

@@ -0,0 +1,24 @@
+rtflite uses third-party Python packages which may be distributed under
+different licenses. We have listed all of these third party packages and
+their licenses below. However, the most up-to-date information can be found
+via inspecting the dependencies field in the pyproject.toml file.
+
+You must agree to the terms of these licenses, in addition to the rtflite
+source code license, in order to use this software.
+
+--------------------------------------------------
+Third party Python packages listed by license type
+[Format: Name - URL]
+--------------------------------------------------
+
+MIT License (https://opensource.org/license/mit)
+  * pydantic - https://github.com/pydantic/pydantic/blob/main/LICENSE
+
+BSD 3-Clause License (https://opensource.org/license/bsd-3-clause)
+  * pandas - https://github.com/pandas-dev/pandas/blob/main/LICENSE
+
+Modified BSD license (https://opensource.org/license/bsd-3-clause)
+  * numpy - https://github.com/numpy/numpy/blob/main/LICENSE.txt
+
+MIT-CMU License (https://opensource.org/license/cmu-license)
+  * pillow - https://github.com/python-pillow/Pillow/blob/main/LICENSE

README.md

@@ -1,2 +1,21 @@
-# rtflite
-Lightweight RTF composer for Python
+# rtflite <img src="docs/assets/logo.png" align="right" width="120" />
+
+Lightweight RTF composer for Python.
+
+Specializes in precise formatting of production-quality tables and figures. Inspired by r2rtf.
+
+## Installation
+
+You can install rtflite from PyPI:
+
+```bash
+pip install rtflite
+```
+
+Or install the development version from GitHub:
+
+```bash
+git clone https://github.com/pharmaverse/rtflite.git
+cd rtflite
+python3 -m pip install -e .
+```

docs/articles/example-baseline.md

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+# Baseline characteristics
+
+
+<!-- `.md` and `.py` files are generated from the `.qmd` file. Please edit that file. -->
+
+!!! tip
+
+    To run the code from this article as a Python script:
+
+    ```bash
+    python3 examples/example-baseline.py
+    ```
+
+This article reproduces `vignettes/example-basechar.Rmd` in the r2rtf
+package.
+
+## Imports
+
+``` python
+from importlib.resources import files
+
+import pandas as pd
+
+import rtflite as rtf
+```
+
+## Ingest data
+
+Load data from CSV file:
+
+``` python
+data_path = files("rtflite.data").joinpath("baseline.csv")
+df = pd.read_csv(data_path, na_filter=False)
+print(df)
+```
+
+                       var         1 1_pct         2 2_pct         3 3_pct      9999 9999_pct    var_label
+    0               Female        53  10.4        50   9.8        40   7.9       143     28.1       Gender
+    1                 Male        33   6.5        34   6.7        44   8.7       111     21.9       Gender
+    2                  <65        14   2.8         8   1.6        11   2.2        33      6.5  Age (Years)
+    3                65-80        42   8.3        47   9.3        55  10.8       144     28.3  Age (Years)
+    4                  >80        30   5.9        29   5.7        18   3.5        77     15.2  Age (Years)
+    5                                                                                          Age (Years)
+    6   Subjects with data        86              84              84             254           Age (Years)
+    7                 Mean      75.2            75.7            74.4            75.1           Age (Years)
+    8                   SD       8.6             8.3             7.9             8.2           Age (Years)
+    9               Median      76.0            77.5            76.0            77.0           Age (Years)
+    10               Range  52 to 89        51 to 88        56 to 88        51 to 89           Age (Years)
+    11               White        78  15.4        78  15.4        74  14.6       230     45.3         Race
+    12               Black         8   1.6         6   1.2         9   1.8        23      4.5         Race
+    13               Other         0   0.0         0   0.0         1   0.2         1      0.2         Race
+
+Create header data frames:
+
+``` python
+header1 = pd.DataFrame([["", "Placebo", "Drug Low Dose", "Drug High Dose", "Total"]])
+header2 = pd.DataFrame([["", "n", "(%)", "n", "(%)", "n", "(%)", "n", "(%)"]])
+```
+
+## Compose RTF
+
+Create RTF document:
+
+``` python
+doc = rtf.RTFDocument(
+    df=df,
+    rtf_title=rtf.RTFTitle(
+        text=["Demographic and Anthropometric Characteristics", "ITT Subjects"]
+    ),
+    rtf_column_header=[
+        rtf.RTFColumnHeader(df=header1, col_rel_width=[3] + [2] * 4),
+        rtf.RTFColumnHeader(
+            df=header2,
+            col_rel_width=[3] + [1.2, 0.8] * 4,
+            border_top=[""] + ["single"] * 8,
+            border_left=["single"] + ["single", ""] * 4,
+        ),
+    ],
+    rtf_body=rtf.RTFBody(
+        page_by=["var_label"],
+        col_rel_width=[3] + [1.2, 0.8] * 4 + [3],
+        text_justification=["l"] + ["c"] * 8 + ["l"],
+        text_format=[""] * 9 + ["b"],
+        border_left=["single"] + ["single", ""] * 4 + ["single"],
+        border_top=[""] * 9 + ["single"],
+        border_bottom=[""] * 9 + ["single"],
+    ),
+)
+
+doc.write_rtf("output.rtf")
+```
+
+## Convert to PDF
+
+``` python
+converter = rtf.LibreOfficeConverter()
+converter.convert(
+    input_files="output.rtf", output_dir=".", format="pdf", overwrite=True
+)
+```
+
+<embed src="../images/example-baseline/output.pdf" style="width:100%; height:400px" type="application/pdf">