Deploying to gh-pages from @ f83d0f2 🚀

_downloads/9911a4d807ac9f1a695f0aa2cf687076/coverage.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" ?>
-<coverage version="7.6.0" timestamp="1721411488088" lines-valid="1494" lines-covered="642" line-rate="0.4297" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
+<coverage version="7.6.0" timestamp="1721424959183" lines-valid="1494" lines-covered="642" line-rate="0.4297" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
 	<!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.6.0 -->
 	<!-- Based on https://raw.githubusercontent.com/cobertura/web/master/htdocs/xml/coverage-04.dtd -->
 	<sources>

_modules/mtbp3/stdcdisc/lib.html

@@ -175,7 +175,7 @@ <h1>Source code for mtbp3.stdcdisc.lib</h1><div class="highlight"><pre>
 <span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span>
     <span class="n">cl</span> <span class="o">=</span> <span class="n">accessLib</span><span class="p">(</span><span class="s2">&quot;/Users/yh2020/cdisc.txt&quot;</span><span class="p">)</span>
     <span class="n">out</span> <span class="o">=</span> <span class="n">cl</span><span class="o">.</span><span class="n">get_ct_list</span><span class="p">()</span>
-    <span class="nb">print</span><span class="p">(</span><span class="n">out</span><span class="p">[</span><span class="s1">&#39;ct&#39;</span><span class="p">])</span>
+    <span class="nb">print</span><span class="p">(</span><span class="n">cl</span><span class="o">.</span><span class="n">ct_list_titles</span><span class="p">)</span>
 </pre></div>
 
            </div>

_sources/std_cdisc.ipynb.txt

@@ -134,6 +134,49 @@
                 "```"
             ]
         },
+        {
+            "cell_type": "markdown",
+            "metadata": {},
+            "source": [
+                "Output:\n",
+                "\n",
+                "```\n",
+                "{'CDASH', 'MRCT', 'COA', 'ADaM', 'Protocol', 'SDTM', 'QRS', 'SEND', 'QS-FT', 'Define-XML', 'Glossary', 'DDF'}\n",
+                "```\n",
+                "\n",
+                "Please note that this page is not executed while building. \n",
+                "Functions and options might be updated as needed.\n",
+                "Please visit API reference page for the newest information on this module."
+            ]
+        },
+        {
+            "cell_type": "markdown",
+            "metadata": {},
+            "source": [
+                "To get the newest protocol ct package information:\n",
+                "\n",
+                "```python\n",
+                "import json\n",
+                "\n",
+                "c = cl.get_ct_package('Protocol')\n",
+                "print(json.dumps(c['package_info'], indent=4))\n",
+                "```\n",
+                "\n",
+                "Output:\n",
+                "\n",
+                "```\n",
+                "{\n",
+                "    \"description\": \"CDISC Controlled Terminology for Protocol is the set of CDISC-developed or CDISC-adopted standard expressions (values) used with data items within CDISC-defined PROTOCOL datasets.\",\n",
+                "    \"effectiveDate\": \"2024-03-29\",\n",
+                "    \"label\": \"Protocol Controlled Terminology Package 57 Effective 2024-03-29\",\n",
+                "    \"name\": \"Protocol CT 2024-03-29\",\n",
+                "    \"source\": \"Protocol Controlled Terminology developed by the CDISC Terminology Team in collaboration with the National Cancer Institute's Enterprise Vocabulary Services (EVS)\",\n",
+                "    \"registrationStatus\": \"Final\",\n",
+                "    \"version\": \"2024-03-29\"\n",
+                "}\n",
+                "```"
+            ]
+        },
         {
             "cell_type": "markdown",
             "metadata": {},

_static/reports/coverage/coverage.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" ?>
-<coverage version="7.6.0" timestamp="1721411488088" lines-valid="1494" lines-covered="642" line-rate="0.4297" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
+<coverage version="7.6.0" timestamp="1721424959183" lines-valid="1494" lines-covered="642" line-rate="0.4297" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
 	<!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.6.0 -->
 	<!-- Based on https://raw.githubusercontent.com/cobertura/web/master/htdocs/xml/coverage-04.dtd -->
 	<sources>

_static/reports/junit/junit.xml

@@ -1 +1 @@
-<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="38" time="8.726" timestamp="2024-07-19T17:51:09.303916" hostname="fv-az1383-254"><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_1df_invalid_input" time="0.002" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_1df_missing_column" time="0.001" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_1df_with_difference" time="0.005" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_1df_without_difference" time="0.002" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_2df_with_existing_column" time="0.010" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_2df_with_non_existing_column" time="0.001" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_2df_with_non_existing_group" time="0.001" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_2df_with_same_group_and_column" time="0.001" /><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_lsr.TestLsrTree" name="test_list_files_dataframe" time="0.001" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_json" time="0.001" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_list" time="0.001" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_string" time="0.000" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_tree" time="0.014" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_tree2" time="0.009" /><testcase classname="tests.test_statlab_corr.TestCorrCalculator" name="test_calculate_kendall_tau_with_dataframe" time="0.002" /><testcase classname="tests.test_statlab_corr.TestCorrCalculator" name="test_calculate_kendall_tau_with_list" time="0.002" /><testcase classname="tests.test_statlab_corr.TestCorrCalculator" name="test_plot_y_list" time="0.017" /><testcase classname="tests.test_statlab_kappa.TestKappaCalculator" name="test_bootstrap_cohen_ci" time="0.229" /><testcase classname="tests.test_statlab_kappa.TestKappaCalculator" name="test_cohen" time="0.077" /><testcase classname="tests.test_statlab_kappa.TestKappaCalculator" name="test_fleiss_kappa" time="0.066" /><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="0.904" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_show_outline_tree" time="0.843" /></testsuite></testsuites>
+<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="38" time="8.907" timestamp="2024-07-19T21:35:40.691822" hostname="fv-az915-703"><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_1df_invalid_input" time="0.002" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_1df_missing_column" time="0.001" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_1df_with_difference" time="0.005" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_1df_without_difference" time="0.002" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_2df_with_existing_column" time="0.009" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_2df_with_non_existing_column" time="0.001" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_2df_with_non_existing_group" time="0.001" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_2df_with_same_group_and_column" time="0.001" /><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="0.193" /><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="0.027" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_dataframe" time="0.001" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_json" time="0.001" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_list" time="0.000" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_string" time="0.000" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_tree" time="0.013" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_tree2" time="0.008" /><testcase classname="tests.test_statlab_corr.TestCorrCalculator" name="test_calculate_kendall_tau_with_dataframe" time="0.002" /><testcase classname="tests.test_statlab_corr.TestCorrCalculator" name="test_calculate_kendall_tau_with_list" time="0.002" /><testcase classname="tests.test_statlab_corr.TestCorrCalculator" name="test_plot_y_list" time="0.016" /><testcase classname="tests.test_statlab_kappa.TestKappaCalculator" name="test_bootstrap_cohen_ci" time="0.234" /><testcase classname="tests.test_statlab_kappa.TestKappaCalculator" name="test_cohen" time="0.067" /><testcase classname="tests.test_statlab_kappa.TestKappaCalculator" name="test_fleiss_kappa" time="0.065" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_compare_file_size" time="0.764" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_get_outline_list" time="0.863" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_show_outline_tree" time="0.832" /></testsuite></testsuites>

example_cdtg.html

@@ -133,7 +133,7 @@ <h1>U/Graph/Categorical Plots Using catPlotter<a class="headerlink" href="#u-gra
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="_images/dada2189c69660b9f69838bd19b56d7a9a86992e5fad7e442c2f47d1faa8e2cb.png" src="_images/dada2189c69660b9f69838bd19b56d7a9a86992e5fad7e442c2f47d1faa8e2cb.png" />
+<img alt="_images/562569dfb30165f52c99bf256d29eda5b25b959ec2da4e82dee42db049811d83.png" src="_images/562569dfb30165f52c99bf256d29eda5b25b959ec2da4e82dee42db049811d83.png" />
 </div>
 </div>
 <p>To create a line plot:</p>
@@ -145,7 +145,7 @@ <h1>U/Graph/Categorical Plots Using catPlotter<a class="headerlink" href="#u-gra
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="_images/59109b26ca0a42fc0242aa9531d320b41d18215103127c81c15237c5e9db8e85.png" src="_images/59109b26ca0a42fc0242aa9531d320b41d18215103127c81c15237c5e9db8e85.png" />
+<img alt="_images/f7a17310b839929dd7cda18a46daf8f9e0ec8068e4c1bf83be7a8aabb842c58d.png" src="_images/f7a17310b839929dd7cda18a46daf8f9e0ec8068e4c1bf83be7a8aabb842c58d.png" />
 </div>
 </div>
 </section>