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yh202109 committed Aug 27, 2024
1 parent 69f48db commit 71c6471
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4 changes: 2 additions & 2 deletions _downloads/214d05cd65dcc9387b037da1ce5a5c33/report.html
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2 changes: 1 addition & 1 deletion _downloads/9911a4d807ac9f1a695f0aa2cf687076/coverage.xml
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6 changes: 3 additions & 3 deletions _sources/std_iso_pdf.ipynb.txt
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Expand Up @@ -143,7 +143,9 @@
},
"outputs": [],
"source": [
"img.show()"
"from IPython.display import Image \n",
"\n",
"display(img)"
]
},
{
Expand All @@ -167,8 +169,6 @@
},
"outputs": [],
"source": [
"from IPython.display import Image \n",
"\n",
"img_path = pfr.get_image(page_index=3, image_index=1, outfolder='.')\n",
"img = Image(filename=img_path)\n",
"display(img)"
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2 changes: 1 addition & 1 deletion _static/reports/coverage/coverage.xml
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<?xml version="1.0" ?>
<coverage version="7.6.1" timestamp="1724795673451" lines-valid="1400" lines-covered="621" line-rate="0.4436" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
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<sources>
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2 changes: 1 addition & 1 deletion _static/reports/junit/junit.xml
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<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="35" time="8.840" timestamp="2024-08-27T21:54:14.642046+00:00" hostname="fv-az732-492"><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="0.197" /><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="0.754" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_get_outline_list" time="0.817" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_show_outline_tree" time="0.883" /><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="0.338" /><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="0.009" /></testsuite></testsuites>
<?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>
4 changes: 2 additions & 2 deletions _static/reports/junit/report.html
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8 changes: 3 additions & 5 deletions example_cdtg.html
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Expand Up @@ -129,15 +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: 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: 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: 10.0% 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.
warnings.warn(msg, UserWarning)
</pre></div>
</div>
<img alt="_images/54eff67918eafa4c112448ad90e1c8389e650a80d60a9279847a6420a33ff6c6.png" src="_images/54eff67918eafa4c112448ad90e1c8389e650a80d60a9279847a6420a33ff6c6.png" />
<img alt="_images/dea08576ac632d4e01b3af0995024cb819a8f253f2240dc3f8c9de5d5ca1fd4e.png" src="_images/dea08576ac632d4e01b3af0995024cb819a8f253f2240dc3f8c9de5d5ca1fd4e.png" />
</div>
</div>
<p>To create a line plot:</p>
Expand All @@ -149,7 +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/8ccda7872b91abb85daa28e758717b81af966ac787600729584b3d3216c7d228.png" src="_images/8ccda7872b91abb85daa28e758717b81af966ac787600729584b3d3216c7d228.png" />
<img alt="_images/50c6abee092d89a44c0467408091f4a4a33c3d3694a147b0077aa2ef5ae84b6f.png" src="_images/50c6abee092d89a44c0467408091f4a4a33c3d3694a147b0077aa2ef5ae84b6f.png" />
</div>
</div>
</section>
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74 changes: 37 additions & 37 deletions example_clinical.html
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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 1 792
1 STD1 TRT1 SUBJ01 VISIT1 2 1558
0 STD1 TRT1 SUBJ01 VISIT1 1 1685
1 STD1 TRT1 SUBJ01 VISIT1 2 1016
</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 1
0 STD1 TRT1 SUBJ01 VISIT1 0 0
1 STD1 TRT1 SUBJ01 VISIT2 0 2

N(1000&lt;=V&lt;=2000) N(all)
0 4 5
1 2 4
0 2 2
1 1 3
</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 6 7 7 20
1 STD1 TRT1 VISIT2 3 6 5 14
2 STD1 TRT1 VISIT3 0 7 3 10
3 STD1 TRT1 VISIT4 2 3 2 7
4 STD1 TRT2 VISIT1 3 11 6 20
5 STD1 TRT2 VISIT2 4 6 6 16
6 STD1 TRT2 VISIT3 2 6 3 11
7 STD1 TRT2 VISIT4 3 2 0 5
8 STD2 TRT1 VISIT1 7 9 4 20
9 STD2 TRT1 VISIT2 2 10 3 15
10 STD2 TRT1 VISIT3 3 7 2 12
11 STD2 TRT1 VISIT4 0 3 3 6
12 STD2 TRT2 VISIT1 5 13 2 20
13 STD2 TRT2 VISIT2 3 9 5 17
14 STD2 TRT2 VISIT3 2 6 2 10
15 STD2 TRT2 VISIT4 2 2 0 4
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
</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 12 23 35 70
1 STD1 TRT1 VISIT2 6 22 25 53
2 STD1 TRT1 VISIT3 0 24 15 39
3 STD1 TRT1 VISIT4 4 9 10 23
4 STD1 TRT2 VISIT1 6 42 30 78
5 STD1 TRT2 VISIT2 8 18 30 56
6 STD1 TRT2 VISIT3 4 20 15 39
7 STD1 TRT2 VISIT4 6 7 0 13
8 STD2 TRT1 VISIT1 14 29 20 63
9 STD2 TRT1 VISIT2 4 37 15 56
10 STD2 TRT1 VISIT3 6 25 10 41
11 STD2 TRT1 VISIT4 0 10 15 25
12 STD2 TRT2 VISIT1 10 48 10 68
13 STD2 TRT2 VISIT2 6 30 25 61
14 STD2 TRT2 VISIT3 4 20 10 34
15 STD2 TRT2 VISIT4 4 6 0 10
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
</pre></div>
</div>
</div>
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