knot from test py errors

dev/symplectic_basis/CuspedCensusData/knot-799.tri

@@ -0,0 +1,91 @@
+% Triangulation
+K9_298
+geometric_solution  6.64250758
+oriented_manifold
+CS_unknown
+
+1 0
+    torus   0.000000000000   0.000000000000
+
+9
+   1    2    1    2 
+ 0132 0132 2310 2310
+   0    0    0    0 
+  0  1  0 -1  0  0  0  0  0  0  0  0  0  0  0  0
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  0 93 -1 -92  0  0  0  0  1  0  0 -1  0  0  0  0
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  0.018380575620   1.764131012569
+
+   0    0    1    1 
+ 0132 3201 2031 1302
+   0    0    0    0 
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  0  0  1 -1  0  0  1 -1  0  1  0 -1 -1  0  1  0
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  0.406844616663   0.131689593298
+
+   0    0    4    3 
+ 3201 0132 0132 0132
+   0    0    0    0 
+  0 -1  0  1  0  0  0  0  1  0  0 -1  0  0  0  0
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  0 -93  0 93  1  0  0 -1 92  0  0 -92  0  0  0  0
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+ -0.719474498994   0.216429183530
+
+   5    6    2    7 
+ 0132 0132 0132 0132
+   0    0    0    0 
+  0  1 -1  0  0  0  0  0  0  0  0  0  0 -1  1  0
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  0 93 -93  0 -1  0  1  0  0  0  0  0  1 -93 92  0
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  0.306785181491   0.933264852110
+
+   6    5    7    2 
+ 2310 3201 0132 0132
+   0    0    0    0 
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  0.306785181491   0.933264852110
+
+   3    5    4    5 
+ 0132 2310 2310 3201
+   0    0    0    0 
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  0  0  0  0  1  0  0 -1 -1  1  0  0  0  0  0  0
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  0.964396181032   1.122233414240
+
+   8    3    4    8 
+ 0132 0132 3201 3201
+   0    0    0    0 
+  0 -1  0  1  0  0  0  0 -1  1  0  0  0  0  0  0
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  0 -93  0 93  0  0  0  0 -93 93  0  0  0  0  0  0
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  0.352636976114   0.338551301107
+
+   7    7    3    4 
+ 1230 3012 0132 0132
+   0    0    0    0 
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  0.827360186786   1.103376573426
+
+   6    6    8    8 
+ 0132 2310 1230 3012
+   0    0    0    0 
+  0  0  0  0  0  0  0  0  0  0  0  0  1 -1  0  0
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  0  0  0  0  0  0  0  0  0  0  0  0 93 -93  0  0
+  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
+  1.713713704742   0.992492876126
+

dev/symplectic_basis/symplectic_basis_main.c

@@ -17,13 +17,13 @@ int main(void) {
     int i, **eqns, num_rows, num_cols;
     Triangulation *theTriangulation;
 
-    int fromFile = 0;
+    int fromFile = 1;
 
     int count = 1;
     int numTet[] = {6};
     int index[] = {774};
 
-    char *error[] = {"CuspedCensusData/link-70k.tri"};
+    char *error[] = {"CuspedCensusData/knot-799.tri"};
 
     char *link[] = {
                     "CuspedCensusData/link-1.tri",

kernel/kernel_code/symplectic_basis.c

@@ -3507,27 +3507,27 @@ void update_adj_curve_along_path(ManifoldBoundary **cusps, OscillatingCurves *cu
     ManifoldBoundary *cusp;
     Triangulation *manifold = cusps[0]->manifold;
 
-//    // Update regions curve data
-//    for (curve = dual_curve_begin->next; curve != dual_curve_end; curve = curve->next)
-//        update_adj_curve_on_cusp(cusps[curve->cusp_index]);
-//
-//    // update endpoint curve data
-//    for (i = 0; i < curve_index; i++) {
-//        // which oscillating curve
-//
-//        for (curve = curves->dual_curve_begin[i].next; curve != &curves->dual_curve_end[i]; curve = curve->next) {
-//            // which component of the curve
-//
-//            for (j = 0; j < 2; j++) {
-//                // which end point
-//
-////                update_adj_curve_at_endpoint(&curve->endpoints[j], dual_curve_begin->next, 0);
-////                update_adj_curve_at_endpoint(&curve->endpoints[j], dual_curve_end->prev, 0);
-//                for (path = dual_curve_begin->next; path != dual_curve_end; path = path->next)
-//                    update_adj_curve_at_endpoint(&curve->endpoints[j], path, 0);
-//            }
-//        }
-//    }
+    // Update regions curve data
+    for (curve = dual_curve_begin->next; curve != dual_curve_end; curve = curve->next)
+        update_adj_curve_on_cusp(cusps[curve->cusp_index]);
+
+    // update endpoint curve data
+    for (i = 0; i < curve_index; i++) {
+        // which oscillating curve
+
+        for (curve = curves->dual_curve_begin[i].next; curve != &curves->dual_curve_end[i]; curve = curve->next) {
+            // which component of the curve
+
+            for (j = 0; j < 2; j++) {
+                // which end point
+
+//                update_adj_curve_at_endpoint(&curve->endpoints[j], dual_curve_begin->next, 0);
+//                update_adj_curve_at_endpoint(&curve->endpoints[j], dual_curve_end->prev, 0);
+                for (path = dual_curve_begin->next; path != dual_curve_end; path = path->next)
+                    update_adj_curve_at_endpoint(&curve->endpoints[j], path, 0);
+            }
+        }
+    }
 
     // update train line endpoints
     for (i = 0; i < manifold->num_cusps; i++) {

venv/bin/docutils

@@ -0,0 +1,8 @@
+#!/home/josh/Documents/Honours-Research-Project/development/SnapPy/venv/bin/python
+# -*- coding: utf-8 -*-
+import re
+import sys
+from docutils.__main__ import main
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())

venv/bin/normalizer

@@ -0,0 +1,8 @@
+#!/home/josh/Documents/Honours-Research-Project/development/SnapPy/venv/bin/python
+# -*- coding: utf-8 -*-
+import re
+import sys
+from charset_normalizer.cli.normalizer import cli_detect
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(cli_detect())

venv/bin/pybabel

@@ -0,0 +1,8 @@
+#!/home/josh/Documents/Honours-Research-Project/development/SnapPy/venv/bin/python
+# -*- coding: utf-8 -*-
+import re
+import sys
+from babel.messages.frontend import main
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())

venv/bin/rst2html.py

@@ -0,0 +1,23 @@
+#!/home/josh/Documents/Honours-Research-Project/development/SnapPy/venv/bin/python
+
+# $Id: rst2html.py 9115 2022-07-28 17:06:24Z milde $
+# Author: David Goodger <[email protected]>
+# Copyright: This module has been placed in the public domain.
+
+"""
+A minimal front end to the Docutils Publisher, producing HTML.
+"""
+
+try:
+    import locale
+    locale.setlocale(locale.LC_ALL, '')
+except Exception:
+    pass
+
+from docutils.core import publish_cmdline, default_description
+
+
+description = ('Generates (X)HTML documents from standalone reStructuredText '
+               'sources.  ' + default_description)
+
+publish_cmdline(writer_name='html', description=description)

venv/bin/rst2html4.py

@@ -0,0 +1,26 @@
+#!/home/josh/Documents/Honours-Research-Project/development/SnapPy/venv/bin/python
+
+# $Id: rst2html4.py 9115 2022-07-28 17:06:24Z milde $
+# Author: David Goodger <[email protected]>
+# Copyright: This module has been placed in the public domain.
+
+"""
+A minimal front end to the Docutils Publisher, producing (X)HTML.
+
+The output conforms to XHTML 1.0 transitional
+and almost to HTML 4.01 transitional (except for closing empty tags).
+"""
+
+try:
+    import locale
+    locale.setlocale(locale.LC_ALL, '')
+except Exception:
+    pass
+
+from docutils.core import publish_cmdline, default_description
+
+
+description = ('Generates (X)HTML documents from standalone reStructuredText '
+               'sources.  ' + default_description)
+
+publish_cmdline(writer_name='html4', description=description)

venv/bin/rst2html5.py

@@ -0,0 +1,33 @@
+#!/home/josh/Documents/Honours-Research-Project/development/SnapPy/venv/bin/python
+# :Copyright: © 2015 Günter Milde.
+# :License: Released under the terms of the `2-Clause BSD license`_, in short:
+#
+#    Copying and distribution of this file, with or without modification,
+#    are permitted in any medium without royalty provided the copyright
+#    notice and this notice are preserved.
+#    This file is offered as-is, without any warranty.
+#
+# .. _2-Clause BSD license: https://opensource.org/licenses/BSD-2-Clause
+#
+# Revision: $Revision: 9021 $
+# Date: $Date: 2022-03-04 16:54:22 +0100 (Fr, 04. Mär 2022) $
+
+"""
+A minimal front end to the Docutils Publisher, producing HTML 5 documents.
+
+The output is also valid XML.
+"""
+
+try:
+    import locale  # module missing in Jython
+    locale.setlocale(locale.LC_ALL, '')
+except locale.Error:
+    pass
+
+from docutils.core import publish_cmdline, default_description
+
+description = ('Generates HTML5 documents from standalone '
+               'reStructuredText sources.\n'
+               + default_description)
+
+publish_cmdline(writer_name='html5', description=description)

venv/bin/rst2latex.py

@@ -0,0 +1,26 @@
+#!/home/josh/Documents/Honours-Research-Project/development/SnapPy/venv/bin/python
+
+# $Id: rst2latex.py 9115 2022-07-28 17:06:24Z milde $
+# Author: David Goodger <[email protected]>
+# Copyright: This module has been placed in the public domain.
+
+"""
+A minimal front end to the Docutils Publisher, producing LaTeX.
+"""
+
+try:
+    import locale
+    locale.setlocale(locale.LC_ALL, '')
+except Exception:
+    pass
+
+from docutils.core import publish_cmdline
+
+description = ('Generates LaTeX documents from standalone reStructuredText '
+               'sources. '
+               'Reads from <source> (default is stdin) and writes to '
+               '<destination> (default is stdout).  See '
+               '<https://docutils.sourceforge.io/docs/user/latex.html> for '
+               'the full reference.')
+
+publish_cmdline(writer_name='latex', description=description)

venv/bin/rst2man.py

@@ -0,0 +1,27 @@
+#!/home/josh/Documents/Honours-Research-Project/development/SnapPy/venv/bin/python
+
+# Author:
+# Contact: [email protected]
+# Copyright: This module has been placed in the public domain.
+
+"""
+man.py
+======
+
+This module provides a simple command line interface that uses the
+man page writer to output from ReStructuredText source.
+"""
+
+import locale
+try:
+    locale.setlocale(locale.LC_ALL, '')
+except Exception:
+    pass
+
+from docutils.core import publish_cmdline, default_description
+from docutils.writers import manpage
+
+description = ("Generates plain unix manual documents.  "
+               + default_description)
+
+publish_cmdline(writer=manpage.Writer(), description=description)

venv/bin/rst2odt.py

@@ -0,0 +1,28 @@
+#!/home/josh/Documents/Honours-Research-Project/development/SnapPy/venv/bin/python
+
+# $Id: rst2odt.py 9115 2022-07-28 17:06:24Z milde $
+# Author: Dave Kuhlman <[email protected]>
+# Copyright: This module has been placed in the public domain.
+
+"""
+A front end to the Docutils Publisher, producing OpenOffice documents.
+"""
+
+try:
+    import locale
+    locale.setlocale(locale.LC_ALL, '')
+except Exception:
+    pass
+
+from docutils.core import publish_cmdline_to_binary, default_description
+from docutils.writers.odf_odt import Writer, Reader
+
+
+description = ('Generates OpenDocument/OpenOffice/ODF documents from '
+               'standalone reStructuredText sources.  ' + default_description)
+
+
+writer = Writer()
+reader = Reader()
+output = publish_cmdline_to_binary(reader=reader, writer=writer,
+                                   description=description)

venv/bin/rst2odt_prepstyles.py

@@ -0,0 +1,20 @@
+#!/home/josh/Documents/Honours-Research-Project/development/SnapPy/venv/bin/python
+
+# Copyright: This module has been placed in the public domain.
+
+"""
+Adapt a word-processor-generated styles.odt for odtwriter use:
+
+Drop page size specifications from styles.xml in STYLE_FILE.odt.
+See https://docutils.sourceforge.io/docs/user/odt.html#page-size
+
+Provisional backwards compatibility stub (to be removed in Docutils >= 0.21).
+
+The actual code moved to the "docutils" library package and can be started
+with ``python -m docutils.writers.odf_odt.prepstyles``.
+"""
+
+from docutils.writers.odf_odt import prepstyles
+
+if __name__ == '__main__':
+    prepstyles.main()

venv/bin/rst2pseudoxml.py

@@ -0,0 +1,23 @@
+#!/home/josh/Documents/Honours-Research-Project/development/SnapPy/venv/bin/python
+
+# $Id: rst2pseudoxml.py 9115 2022-07-28 17:06:24Z milde $
+# Author: David Goodger <[email protected]>
+# Copyright: This module has been placed in the public domain.
+
+"""
+A minimal front end to the Docutils Publisher, producing pseudo-XML.
+"""
+
+try:
+    import locale
+    locale.setlocale(locale.LC_ALL, '')
+except Exception:
+    pass
+
+from docutils.core import publish_cmdline, default_description
+
+
+description = ('Generates pseudo-XML from standalone reStructuredText '
+               'sources (for testing purposes).  ' + default_description)
+
+publish_cmdline(description=description)