Release v0.3.0 · A2-ai/reportifyr

New Features

config.yaml now included with the package and allows for greater control over reportifyr content.
- config.yaml contents are summarized below:
  - Report configuration:
    - report_dir_name captures the report directory name when calling initialize_report_project().
    - outputs_dir_name captures the OUTPUTS directory name when calling initialize_report_project().
    - strict if true, errors if duplicate figures/tables are found in document. If false, duplicate figures will be inserted as duplicates, but only the first instance of a duplicate table is inserted.
  - Table configuration:
    - save_table_rtf if true, saves table artifacts as .RTF in addition to .csv/.RDS.
  - Figure configuration:
    - fig_alignment [center/left/right] sets the alignment of the figure inserted into the document.
    - use_embedded_dimensions if true, captures the size of the reportifyr figures within the document and maintains this size when updating artifact.
    - use_artifact_size if true, uses the size of the saved artifact for dimensions when inserting the figure.
    - default_fig_width sets the default width (inches) to use for figures. Aspect ratio is maintained from saved artifact.
    - label_multi_figures if true, for multi-figure insertion (see below) adds a figure label (A, B, C, etc.) to upper left corner of figures before inserting into the document.
  - Footnote configuration:
    - font can be set through the footnotes_font field.
    - font size can be set through the footnotes_font_size field.
    - use_object_path_as_source if true, sets the source footnote to use the path to the artifact instead of the script that generated it. Default setting is false.
    - wrap_path_in_[] controls whether source/object footnotes are written as [path/to/source.R] (true) or path/to/source.R (false). Default setting is true.
    - combine_duplicate_footnotes if true, for multi-figure insertion (more below), only the first instance of duplicated footnotes will be inserted. To use, label_multi_figures must be set to false.
    - footnote_order sets the ordering of footnotes within the document.
- validate_config(path_to_config_yaml) function is included to ensure config is compatible with reportifyr.
  - All expected fields are checked for correct type and valid options for non-boolean fields. Any errors are surfaced to the user. Any additional fields not used in reportifyr are ignored.
    - Examples:
      > validate_config(here::here("inst/extdata/config.yaml")) 2025-04-11 09:54:53 [ERROR] footnotes_font_size should be integer/double, not: character 2025-04-11 09:54:53 [ERROR] Unexpected footnote field: source, object, notes, abbreviations. Acceptable fields are: Object, Source, Notes, Abbreviations 2025-04-11 09:54:53 [ERROR] Unexpected figure alignment option: middle. Acceptable alignments are: center, left, right [1] FALSE
      fixing the capitalization on footnote_order, setting fig_alignment to one of [center/left/right], and making footnotes_font_size numeric gives the following result:
      > validate_config(here::here("inst/extdata/config.yaml")) [1] `true`

initialize_report_project has two new arguments report_dir_name and outputs_dir_name.

report_dir_name sets the name/structure of where the report will be generated.
outputs_dir_name sets the name/structure of where the report artifacts will be saved.

Examples:

You can provide nested directories to further organize a project that might have multiple reports. Here we create two reports one in report/PK and one in report/NCA and similarly separate the outputs into two subdirectories.

> initialize_report_project(here::here(), report_dir_name = "reports/PK", outputs_dir_name = "outputs/PK")
If uv, Python, and Python dependencies (python-docx, PyYAML, Pillow)

are not installed, this will install them.

Otherwise, the installed versions will be used.

Are you sure you want to continue? [Y/n]
y
Creating python virtual environment with the following settings:
        venv_dir: /Users/user/Documents/reportifyr_project
        python-docx.version: 1.1.2
        pyyaml.version: 6.0.2
        pillow.version: 11.1.0
        uv.version: 0.7.8
        python.version: 3.13.2
uv already installed
Created venv at /Users/user/Documents/reportifyr_project/.venv
Installed python-docx v1.1.2
Installed pyyaml v6.0.2
Installed pillow v11.1.0

copied standard_footnotes.yaml into /Users/user/Documents/reportifyr_project/reports/PK
copied config.yaml into /Users/user/Documents/reportifyr_project/reports/PK

> initialize_report_project(here::here(), report_dir_name = "reports/NCA", outputs_dir_name = "outputs/NCA")
If uv, Python, and Python dependencies (python-docx, PyYAML, Pillow)

are not installed, this will install them.

Otherwise, the installed versions will be used.

Are you sure you want to continue? [Y/n]
y
uv already installed
venv already exists at /Users/user/Documents/reportifyr_project/.venv
Current python-docx version: 1.1.2
python-docx already at correct version (v1.1.2)
Current pyyaml version: 6.0.2
pyyaml already at correct version (v6.0.2)
Current pillow version: 11.1.0
pillow already at correct version (v11.1.0)

copied standard_footnotes.yaml into /Users/user/Documents/reportifyr_project/reports/NCA
copied config.yaml into /Users/user/Documents/reportifyr_project/reports/NCA

This creates the following directory structure

.
├── outputs
│   ├── NCA
│   │   ├── figures
│   │   ├── listings
│   │   └── tables
│   └── PK
│       ├── figures
│       ├── listings
│       └── tables
└── reports
    ├── NCA
    │   ├── config.yaml
    │   ├── draft
    │   ├── final
    │   ├── scripts
    │   ├── shell
    │   └── standard_footnotes.yaml
    └── PK
        ├── config.yaml
        ├── draft
        ├── final
        ├── scripts
        ├── shell
        └── standard_footnotes.yaml

initialize_report_project() also creates a initialization .json file using the report_dir_name to store metadata about the report project setup.

Example reports_NCA_init.json created from the above initialize_report_project call:

{
  "creation_timestamp": "2025-04-11 10:14:29",
  "last_modified": "2025-04-11 10:14:29",
  "user": "user",
  "config": {
    "report_dir_name": "reports/NCA",
    "outputs_dir_name": "outputs/NCA",
    "footnotes_font": "Arial Narrow",
    "footnotes_font_size": "10",
    "use_object_path_as_source": false,
    "wrap_path_in_[]": true,
    "combine_duplicate_footnotes": true,
    "footnote_order": ["source", "object", "notes", "abbreviations"],
    "save_table_rtf": false,
    "fig_alignment": "middle",
    "use_artifact_size": true,
    "default_fig_width": 6,
    "use_embedded_dimensions": true,
    "label_multi_figures": false
  },
  "python_versions": {
    "venv_dir": "/Users/user/Documents/reportifyr_project",
    "python-docx.version": "1.1.2",
    "pyyaml.version": "6.0.2",
    "pillow.version": "11.1.0",
    "uv.version": "0.7.8",
    "python.version": "3.13.2"
  }
}

sync_report_project(project_dir, report_dir_name) has been added to synchronize the report project with both the config.yaml and any Python dependency versions set with options() to ensure that reportifyr is using the desired specifications. sync_report_project() consults the initialization file, options, and config.yaml to bring them to a consistent state, updating the init file if needed.

Example:

> options("python-docx.version" = "1.1.1")
> sync_report_project(here::here(), "reports/NCA")
Python dependency versions have been changed, updating /Users/user/Documents/reportifyr_project/.reports_NCA_init.json
uv already installed
venv already exists at /Users/user/Documents/reportifyr_project/.venv
Current python-docx version: 1.1.2
Updating python-docx from v1.1.2 to v1.1.1
Installed python-docx v1.1.1
Current pyyaml version: 6.0.2
pyyaml already at correct version (v6.0.2)
Current pillow version: 11.1.0
pillow already at correct version (v11.1.0)

validate_document(docx_in, config_yaml) has been added to check that the document is in a format compatible with reportifyr use. Magic strings within docx_in are checked for duplicate artifacts and warns/errors (depending on strict config) user about duplicates.

Magic String Updates:

Multiple figures (multi-figure) with a single combined footnote can now be added with the following syntax:

Figure 1: Multiple figures with single footnote.

{rpfy}:[figure_1.png, figure_2.png].

The resulting document after build_report() will look like the following:

Figure 1: Multiple figures with single footnote.

{rpfy}:[figure_1.png, figure_2.png].

A[Figure 1]

B[Figure 2]

Source: A: path/to/figure_1_source.R Timestamp. B: path/to/figure_2_source.R Timestamp.

Notes: A: notes for figure A. B: notes for figure B.

Abbreviations: A: N/A, B: N/A.
- If label_multi_figures is set to true in the config.yaml, figure labels will be added to each figure on the top left corner before insertion.
 (Example: Label 'A' on figure_1, Label 'B' on figure_2). Each footnote will be denoted with respective labels (A/B) before combining into one 'Notes' line.
 This will work for any number of figures, with the labels wrapping to AA, AB after Z, if necessary. If label_multi_figures is not in config.yaml the default is
 false, and the images will not be labeled (accordingly, footnotes will not have the A/B/etc. label).
Below is an example of multiple image insertion with label_multi_figures set to false and combine_duplicate_footnotes set to true:
```
Figure 1: Multiple figures with single footnote. 
{rpfy}:[figure_1.png, figure_2.png]. 
[Figure 1] 
[Figure 2] 
Source: path/to/figure_1_source.R Timestamp. path/to/figure_2_source.R Timestamp. 
Notes: notes for figure A. notes for figure B. 
Abbreviations: N/A. 
 
Note: If source/notes are the same they will also be combined into one entry.
```
- Alternatively, multiple figures with multiple footnotes can also be inserted under a figure caption with:
 
 Figure 2: Some caption for multiple figures
 
 {rpfy}:figure_1.png
 
 {rpfy}:figure_2.png
 - The resulting document after build_report() will look like:
 
 Figure 2: Some caption for multiple figures.
 
 {rpfy}:figure_1.png
 
 [Figure 1]
 
 [Footnote for Figure 1]
 
 {rpfy}:figure_2.png
 
 [Figure 2]
 
 [Footnote for Figure 2]
- Users can now supply per-figure sizing options with angled brackets: {rpfy}:figure.png<width: 3.67, height: 5.32>. This syntax will cause reportifyr to insert figure.png into the document and resize to 3.67 in by 5.32 in. You can also specify options in multi-figure input {rpfy}:[figure1.png<width: 3, height: 4>, figure2.png<width: 4, height: 4>] and each figure will be inserted at the specified dimensions.
- With use_embedded_dimensions set to true in your config.yaml, upon updating a report, when figures are removed their dimensions are captured and added to the magic string and used on insertion of the updated figure. You can then resize an image from its saved dimension and the resizing will persist throughout the document life cycle.
Magic strings are now embedded in the alt text of each figure or table (when calling add_plots or add_tables) using the respective add_plots_alt_text() or add_tables_alt_text().
- validate_alt_text_magic_strings() compares these stored values to the inline magic strings to catch any potential discrepancies.

Footnote Updates

Footnotes now support subscript and superscript using LaTeX-like syntax: AUC_{0-24} will show up in the rendered .docx with 0-24 as a subscript, and kg/m^{2} will show up with the 2 as a superscript.
The source footnote now reports the last time the source was committed to Git. If you are not using Git, it will use the time that the footnote was inserted at, while object footnote reports the time of artifact creation.

Minor Improvements

uv has been been updated from version 0.5.1 to 0.7.8.

Messaging on package load has been reworked:

ℹ Loading reportifyr
── Set reportifyr options ────────────────────────────────────────────────────────────────────────────────
✔ Using installed uv version 0.7.8
── venv options ──────────────────────────────────────────────────────────────────────────────────────────
▇ Using project root for venv (unless already present), set options('venv_dir') to change
── Version options ───────────────────────────────────────────────────────────────────────────────────────
▇ Using system python version, set options('python.version') to change
▇ Using python-docx version 1.1.2, set options('python-docx.version') to change
▇ Using pyyaml version 6.0.2, set options('pyyaml.version') to change
▇ Using pillow v11.1.0, set options('pillow.version') to change

Messaging around venv/uv/Python dependencies has been reworked:

> initialize_report_project(here::here())
If uv, Python, and Python dependencies (python-docx, PyYAML, Pillow)

are not installed, this will install them.

Otherwise, the installed versions will be used.

Are you sure you want to continue? [Y/n]
y
Creating python virtual environment with the following settings:
        venv_dir: /path/to/project/
        python-docx.version: 1.1.2
        pyyaml.version: 6.0.2
        pillow.version: 11.1.0
        uv.version: 0.7.8
        python.version:  3.13.2
uv already installed
Created venv at /path/to/project/.venv
Installed python-docx v1.1.2
Installed pyyaml v6.0.2
Installed pillow v11.1.0

copied standard_footnotes.yaml into /path/to/project/report
copied config.yaml into /path/to/project/report

Python dependency versions are now recorded in a .json file saved in project/<report_dir_name>/.python_dependency_versions.json to improve traceability.

// WARNING: This file is automatically generated on initialization. Do not edit by hand!
{
  "venv_dir": "/Users/user/Documents/reportifyr_project",
  "python-docx.version": "1.1.2",
  "pyyaml.version": "6.0.2",
  "pillow.version": "11.1.0",
  "uv.version": "0.7.8",
  "python.version": "3.13.2"
}

toggle_logger() now displays the logging level at which it’s operating.
add_tables() and add_plots() now keep the artifact caption and magic string on the same page of the artifact instead of being broken across pages in some situations.
get_venv_uv_paths() returns both venv and uv paths as a convenient helper function.

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v0.3.0

New Features

Magic String Updates:

Footnote Updates

Minor Improvements

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