.rds were not being processed correctly by add_tables().docx_out = NULL for build_report() was failing within validate_input_args().write_object_metadata() during a quarto render was being captured as the intermediate .rmarkdown.uv installation, ensuring the setup script now works on both Unix-like (Unix/Mac) and Windows platforms.uv version check such that the installed version is compared against requested version before installing requested version..python_dependency_version.json in .venv not being propagated to the .python_dependency_version.json in report_dir_name.python.version via options('python.version') was creating a new line in both .python_dependency_version.json files.If config_yaml is left NULL for the following functions, a default config.yaml file bundled with reportifyr is used instead:
add_footnotes()add_plots()add_tables()build_report()finalize_document()remove_tables_figures_footnotes()validate_input_args() and validate_alt_text_magic_strings() no longer take a config_yaml argument.
Function and argument descriptions introduced or expanded on in 0.3.0 have been updated for clarity and understanding.
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:
footnotes_font field.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.
> 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
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.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
.
├── 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.
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.
> 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.
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.
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.<br>
{rpfy}:[figure_1.png, figure_2.png].<br>
[Figure 1]<br>
[Figure 2]<br>
Source: path/to/figure_1_source.R Timestamp. path/to/figure_2_source.R Timestamp.<br>
Notes: notes for figure A. notes for figure B.<br>
Abbreviations: N/A.<br>
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
build_report() will look like: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.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.
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.