Skip to content

Commit

Permalink
Deploying to gh-pages from @ 02cdccc 🚀
Browse files Browse the repository at this point in the history
  • Loading branch information
@yh202109
yh202109 committed Aug 27, 2024
1 parent 71c6471 commit d6f68ea
Show file tree
Hide file tree
Showing 19 changed files with 245 additions and 192 deletions.
6 changes: 3 additions & 3 deletions _downloads/214d05cd65dcc9387b037da1ce5a5c33/report.html
View file

Large diffs are not rendered by default.

2 changes: 1 addition & 1 deletion _downloads/9911a4d807ac9f1a695f0aa2cf687076/coverage.xml
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<?xml version="1.0" ?>
<coverage version="7.6.1" timestamp="1724795998517" lines-valid="1400" lines-covered="621" line-rate="0.4436" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
<coverage version="7.6.1" timestamp="1724796721828" lines-valid="1400" lines-covered="621" line-rate="0.4436" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
<!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.6.1 -->
<!-- Based on https://raw.githubusercontent.com/cobertura/web/master/htdocs/xml/coverage-04.dtd -->
<sources>
Expand Down
Binary file removed _images/2973dff4b153b750c37e9aa3fb18981b1ae9455832391354ce31f681e242b511.png
View file
Binary file not shown.
Binary file removed _images/50c6abee092d89a44c0467408091f4a4a33c3d3694a147b0077aa2ef5ae84b6f.png
View file
Binary file not shown.
Binary file added _images/51fc3f45360f9decdc70855e20a2195d5989f6394f50d9941a3b93ad374c6a2f.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file removed _images/82a80f6732141d124f9a143f9e5340c3e34672a55194207f160f1dd60d1ef0f0.png
View file
Binary file not shown.
Binary file removed _images/dea08576ac632d4e01b3af0995024cb819a8f253f2240dc3f8c9de5d5ca1fd4e.png
View file
Binary file not shown.
Binary file added _images/ff438b95cf2a4d453597747839807ae464eec93c899d8b9832b856b6e1947ba7.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
9 changes: 7 additions & 2 deletions _sources/std_iso_pdf.ipynb.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -64,6 +64,8 @@
}
},
"source": [
"## PDF File Summary\n",
"\n",
"To use `mtbp3.stdiso`:"
]
},
Expand Down Expand Up @@ -115,6 +117,8 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## Image \n",
"\n",
"We can see that there is one image in the 3rd page from the summary above. \n",
"To extract the first image on the 3rd page:"
]
Expand Down Expand Up @@ -145,6 +149,7 @@
"source": [
"from IPython.display import Image \n",
"\n",
"img.resize(width=300)\n",
"display(img)"
]
},
Expand All @@ -156,7 +161,7 @@
}
},
"source": [
"To save the image to a file, add an existing folder path using `outfolder='add_path_here'`."
"To save the 2nd image on the 4th page to a file, add an existing folder path using `outfolder='add_path_here'`:"
]
},
{
Expand All @@ -170,7 +175,7 @@
"outputs": [],
"source": [
"img_path = pfr.get_image(page_index=3, image_index=1, outfolder='.')\n",
"img = Image(filename=img_path)\n",
"img = Image(filename=img_path, width=300)\n",
"display(img)"
]
},
Expand Down
2 changes: 1 addition & 1 deletion _static/reports/coverage/coverage.xml
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<?xml version="1.0" ?>
<coverage version="7.6.1" timestamp="1724795998517" lines-valid="1400" lines-covered="621" line-rate="0.4436" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
<coverage version="7.6.1" timestamp="1724796721828" lines-valid="1400" lines-covered="621" line-rate="0.4436" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
<!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.6.1 -->
<!-- Based on https://raw.githubusercontent.com/cobertura/web/master/htdocs/xml/coverage-04.dtd -->
<sources>
Expand Down
2 changes: 1 addition & 1 deletion _static/reports/junit/junit.xml
View file
Original file line number Diff line number Diff line change
@@ -1 +1 @@
<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="35" time="8.474" timestamp="2024-08-27T21:59:40.055324+00:00" hostname="fv-az530-511"><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_find_section_given_words" time="0.001" /><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_find_section_given_words_invalid_include" time="0.001" /><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_find_section_given_words_invalid_outfmt" time="0.001" /><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_load_list" time="0.001" /><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_show_ctoc_tree" time="0.201" /><testcase classname="tests.test_health_emt.TestEmt" name="test_expected_file_lists" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_files" time="0.005" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_hlgt" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_hlt" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_llt" time="0.007" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_pt" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_pt_given_soc" time="0.006" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_pt_given_soc_primary_only" time="0.006" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_soc" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_list_files" time="0.025" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_compare_file_size" time="0.757" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_get_outline_list" time="0.778" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_show_outline_tree" time="0.885" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_1df_invalid_input" time="0.001" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_1df_missing_column" time="0.001" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_1df_with_difference" time="0.004" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_1df_without_difference" time="0.002" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_2df_with_existing_column" time="0.009" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_2df_with_non_existing_column" time="0.001" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_2df_with_non_existing_group" time="0.001" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_2df_with_same_group_and_column" time="0.001" /><testcase classname="tests.test_util_cdtg.TestCatPlotter" name="test_boxplot" time="0.394" /><testcase classname="tests.test_util_cdtg.TestCatPlotter" name="test_lineplot" time="0.339" /><testcase classname="tests.test_util_cdtg.TestCatPlotter" name="test_update_parameters" time="0.001" /><testcase classname="tests.test_util_lsr.TestLsrTree" name="test_list_files_dataframe" time="0.001" /><testcase classname="tests.test_util_lsr.TestLsrTree" name="test_list_files_json" time="0.001" /><testcase classname="tests.test_util_lsr.TestLsrTree" name="test_list_files_list" time="0.001" /><testcase classname="tests.test_util_lsr.TestLsrTree" name="test_list_files_string" time="0.000" /><testcase classname="tests.test_util_lsr.TestLsrTree" name="test_list_files_tree" time="0.013" /><testcase classname="tests.test_util_lsr.TestLsrTree" name="test_list_files_tree2" time="0.008" /></testsuite></testsuites>
<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="35" time="9.225" timestamp="2024-08-27T22:11:42.534743+00:00" hostname="fv-az1249-914"><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_find_section_given_words" time="0.001" /><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_find_section_given_words_invalid_include" time="0.001" /><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_find_section_given_words_invalid_outfmt" time="0.001" /><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_load_list" time="0.001" /><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_show_ctoc_tree" time="0.202" /><testcase classname="tests.test_health_emt.TestEmt" name="test_expected_file_lists" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_files" time="0.005" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_hlgt" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_hlt" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_llt" time="0.007" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_pt" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_pt_given_soc" time="0.006" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_pt_given_soc_primary_only" time="0.006" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_soc" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_list_files" time="0.025" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_compare_file_size" time="0.775" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_get_outline_list" time="0.801" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_show_outline_tree" time="0.928" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_1df_invalid_input" time="0.001" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_1df_missing_column" time="0.001" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_1df_with_difference" time="0.004" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_1df_without_difference" time="0.002" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_2df_with_existing_column" time="0.009" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_2df_with_non_existing_column" time="0.001" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_2df_with_non_existing_group" time="0.001" /><testcase classname="tests.test_util_cdt.TestCdt" name="test_diff_2cols_in_2df_with_same_group_and_column" time="0.001" /><testcase classname="tests.test_util_cdtg.TestCatPlotter" name="test_boxplot" time="0.396" /><testcase classname="tests.test_util_cdtg.TestCatPlotter" name="test_lineplot" time="0.339" /><testcase classname="tests.test_util_cdtg.TestCatPlotter" name="test_update_parameters" time="0.001" /><testcase classname="tests.test_util_lsr.TestLsrTree" name="test_list_files_dataframe" time="0.001" /><testcase classname="tests.test_util_lsr.TestLsrTree" name="test_list_files_json" time="0.001" /><testcase classname="tests.test_util_lsr.TestLsrTree" name="test_list_files_list" time="0.001" /><testcase classname="tests.test_util_lsr.TestLsrTree" name="test_list_files_string" time="0.000" /><testcase classname="tests.test_util_lsr.TestLsrTree" name="test_list_files_tree" time="0.013" /><testcase classname="tests.test_util_lsr.TestLsrTree" name="test_list_files_tree2" time="0.008" /></testsuite></testsuites>
6 changes: 3 additions & 3 deletions _static/reports/junit/report.html
View file

Large diffs are not rendered by default.

8 changes: 4 additions & 4 deletions example_cdtg.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -129,13 +129,13 @@ <h1>U/Graph/Categorical Plots Using catPlotter<a class="headerlink" href="#u-gra
</div>
</div>
<div class="cell_output docutils container">
<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/home/runner/.cache/pypoetry/virtualenvs/mtbp3-STzYEG9e-py3.10/lib/python3.10/site-packages/seaborn/categorical.py:3399: UserWarning: 10.0% of the points cannot be placed; you may want to decrease the size of the markers or use stripplot.
<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/home/runner/.cache/pypoetry/virtualenvs/mtbp3-STzYEG9e-py3.10/lib/python3.10/site-packages/seaborn/categorical.py:3399: UserWarning: 11.1% of the points cannot be placed; you may want to decrease the size of the markers or use stripplot.
warnings.warn(msg, UserWarning)
/home/runner/.cache/pypoetry/virtualenvs/mtbp3-STzYEG9e-py3.10/lib/python3.10/site-packages/seaborn/categorical.py:3399: UserWarning: 15.0% of the points cannot be placed; you may want to decrease the size of the markers or use stripplot.
/home/runner/.cache/pypoetry/virtualenvs/mtbp3-STzYEG9e-py3.10/lib/python3.10/site-packages/seaborn/categorical.py:3399: UserWarning: 45.0% of the points cannot be placed; you may want to decrease the size of the markers or use stripplot.
warnings.warn(msg, UserWarning)
</pre></div>
</div>
<img alt="_images/dea08576ac632d4e01b3af0995024cb819a8f253f2240dc3f8c9de5d5ca1fd4e.png" src="_images/dea08576ac632d4e01b3af0995024cb819a8f253f2240dc3f8c9de5d5ca1fd4e.png" />
<img alt="_images/ff438b95cf2a4d453597747839807ae464eec93c899d8b9832b856b6e1947ba7.png" src="_images/ff438b95cf2a4d453597747839807ae464eec93c899d8b9832b856b6e1947ba7.png" />
</div>
</div>
<p>To create a line plot:</p>
Expand All @@ -147,7 +147,7 @@ <h1>U/Graph/Categorical Plots Using catPlotter<a class="headerlink" href="#u-gra
</div>
</div>
<div class="cell_output docutils container">
<img alt="_images/50c6abee092d89a44c0467408091f4a4a33c3d3694a147b0077aa2ef5ae84b6f.png" src="_images/50c6abee092d89a44c0467408091f4a4a33c3d3694a147b0077aa2ef5ae84b6f.png" />
<img alt="_images/51fc3f45360f9decdc70855e20a2195d5989f6394f50d9941a3b93ad374c6a2f.png" src="_images/51fc3f45360f9decdc70855e20a2195d5989f6394f50d9941a3b93ad374c6a2f.png" />
</div>
</div>
</section>
Expand Down
76 changes: 38 additions & 38 deletions example_clinical.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -127,8 +127,8 @@ <h2>Example 1<a class="headerlink" href="#example-1" title="Link to this heading
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> study treatment subject visit meal calorie
0 STD1 TRT1 SUBJ01 VISIT1 1 1685
1 STD1 TRT1 SUBJ01 VISIT1 2 1016
0 STD1 TRT1 SUBJ01 VISIT1 1 1515
1 STD1 TRT1 SUBJ01 VISIT1 2 636
</pre></div>
</div>
</div>
Expand All @@ -145,12 +145,12 @@ <h2>Example 1<a class="headerlink" href="#example-1" title="Link to this heading
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> study treatment subject visit N(0&lt;=X&lt;500) N(500&lt;=X&lt;1000) \
0 STD1 TRT1 SUBJ01 VISIT1 0 0
1 STD1 TRT1 SUBJ01 VISIT2 0 2
0 STD1 TRT1 SUBJ01 VISIT1 0 1
1 STD1 TRT1 SUBJ02 VISIT1 0 1

N(1000&lt;=V&lt;=2000) N(all)
0 2 2
1 1 3
0 2 3
1 1 2
</pre></div>
</div>
</div>
Expand All @@ -165,22 +165,22 @@ <h2>Example 1<a class="headerlink" href="#example-1" title="Link to this heading
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> study treatment visit N(0&lt;=X&lt;3) N(3&lt;=X&lt;5) N(5&lt;=V&lt;=7) N(all)
0 STD1 TRT1 VISIT1 5 12 3 20
1 STD1 TRT1 VISIT2 3 7 4 14
2 STD1 TRT1 VISIT3 3 3 5 11
3 STD1 TRT1 VISIT4 0 3 1 4
4 STD1 TRT2 VISIT1 7 11 2 20
5 STD1 TRT2 VISIT2 3 4 6 13
6 STD1 TRT2 VISIT3 4 2 3 9
7 STD1 TRT2 VISIT4 2 2 0 4
8 STD2 TRT1 VISIT1 2 9 9 20
9 STD2 TRT1 VISIT2 3 9 3 15
10 STD2 TRT1 VISIT3 1 7 2 10
11 STD2 TRT1 VISIT4 2 3 1 6
12 STD2 TRT2 VISIT1 5 10 5 20
13 STD2 TRT2 VISIT2 3 6 3 12
14 STD2 TRT2 VISIT3 1 3 3 7
15 STD2 TRT2 VISIT4 0 3 1 4
0 STD1 TRT1 VISIT1 4 13 3 20
1 STD1 TRT1 VISIT2 3 11 2 16
2 STD1 TRT1 VISIT3 5 4 2 11
3 STD1 TRT1 VISIT4 1 3 2 6
4 STD1 TRT2 VISIT1 8 7 5 20
5 STD1 TRT2 VISIT2 2 4 8 14
6 STD1 TRT2 VISIT3 2 8 2 12
7 STD1 TRT2 VISIT4 1 4 2 7
8 STD2 TRT1 VISIT1 4 14 2 20
9 STD2 TRT1 VISIT2 3 10 4 17
10 STD2 TRT1 VISIT3 1 7 3 11
11 STD2 TRT1 VISIT4 1 3 1 5
12 STD2 TRT2 VISIT1 5 11 4 20
13 STD2 TRT2 VISIT2 4 9 2 15
14 STD2 TRT2 VISIT3 0 8 2 10
15 STD2 TRT2 VISIT4 2 2 1 5
</pre></div>
</div>
</div>
Expand All @@ -194,22 +194,22 @@ <h2>Example 1<a class="headerlink" href="#example-1" title="Link to this heading
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> study treatment visit Sum(0&lt;=X&lt;3) Sum(3&lt;=X&lt;5) Sum(5&lt;=V&lt;=7) Sum(all)
0 STD1 TRT1 VISIT1 10 43 15 68
1 STD1 TRT1 VISIT2 6 23 20 49
2 STD1 TRT1 VISIT3 6 11 25 42
3 STD1 TRT1 VISIT4 0 11 5 16
4 STD1 TRT2 VISIT1 14 38 10 62
5 STD1 TRT2 VISIT2 6 15 30 51
6 STD1 TRT2 VISIT3 8 7 15 30
7 STD1 TRT2 VISIT4 4 8 0 12
8 STD2 TRT1 VISIT1 4 30 45 79
9 STD2 TRT1 VISIT2 6 35 15 56
10 STD2 TRT1 VISIT3 2 25 10 37
11 STD2 TRT1 VISIT4 4 11 5 20
12 STD2 TRT2 VISIT1 10 34 25 69
13 STD2 TRT2 VISIT2 6 19 15 40
14 STD2 TRT2 VISIT3 2 11 15 28
15 STD2 TRT2 VISIT4 0 12 5 17
0 STD1 TRT1 VISIT1 8 46 15 69
1 STD1 TRT1 VISIT2 6 36 10 52
2 STD1 TRT1 VISIT3 10 14 10 34
3 STD1 TRT1 VISIT4 2 11 10 23
4 STD1 TRT2 VISIT1 16 25 25 66
5 STD1 TRT2 VISIT2 4 14 40 58
6 STD1 TRT2 VISIT3 4 29 10 43
7 STD1 TRT2 VISIT4 2 15 10 27
8 STD2 TRT1 VISIT1 8 48 10 66
9 STD2 TRT1 VISIT2 6 35 20 61
10 STD2 TRT1 VISIT3 2 26 15 43
11 STD2 TRT1 VISIT4 2 12 5 19
12 STD2 TRT2 VISIT1 10 39 20 69
13 STD2 TRT2 VISIT2 8 33 10 51
14 STD2 TRT2 VISIT3 0 28 10 38
15 STD2 TRT2 VISIT4 4 6 5 15
</pre></div>
</div>
</div>
Expand Down
Loading

0 comments on commit d6f68ea

Please sign in to comment.