Merge pull request #25 from thecaligarmo/develop

Merge in Develop

.github/workflows/py-lint.yml

@@ -35,7 +35,7 @@ jobs:
     - name: Install relint
       run: pip install tox relint
     - name: Lint using relint
-      run: tox -e relint -- src/sage/
+      run: tox -e relint -- oriented_matroids
   lint-rst:
     name: Validate docstring markup as RST
     runs-on: ubuntu-latest

.gitignore

@@ -87,3 +87,6 @@ ENV/
 
 # Rope project settings
 .ropeproject
+
+# vim stuff
+*.swp

.relint.yml

@@ -0,0 +1,63 @@
+# From https://github.com/sagemath/sage-patchbot/blob/master/sage_patchbot/plugins.py
+# (simple pattern-exclusion plugins)
+# The patterns have been edited slightly because relint tests the regexp to the whole file,
+# whereas the patchbots tests them line by line.
+
+- name: 'python3: Python3 incompatible code'
+  hint: |
+    # ifilter, imap, izip           # __metaclass__
+    # update raise statements       # except Exception, var
+    # six is no longer allowed
+  pattern: '(import.*[, ]ifilter|import.*[, ]imap|import.*[, ]izip|^\s*raise\s*[A-Za-z]*Error\s*,|__metaclass__|except\s*[A-Za-z]\s*,|import six|from six import)'
+  filePattern: .*[.](py|pyx|rst)
+
+- name: 'foreign_latex: foreign commands in LaTeX'
+  hint: |
+    use equivalent LaTeX commands instead of plain TeX commands such as \over, \choose, etc.
+  pattern: '(\\choose|\\atop|\\above|\\overwithdelims|\\atopwithdelims|\\abovewithdelims)'
+  # \over appears in bad latex code coming from Fricas and Maxima
+
+- name: 'blocks: wrong syntax for blocks (INPUT, OUTPUT, EXAMPLES, NOTE, etc.)'
+  hint: |
+    # the correct syntax is .. SEEALSO::
+    # TESTS and EXAMPLES should be plural, NOTE singular
+    # no :: after INPUT, OUTPUT, REFERENCE blocks
+    # no " :" at the end of lines
+  pattern: '(\.\.SEE|SEE ALSO|SEEALSO:($|[^:])|^\s*TEST:|^\s*EXAMPLE:|^\s*NOTES:|^\s*[A-Z]*PUT::|^\s*REFERENCES?::$)'
+
+- name: 'trac_links: bad trac link'
+  hint: |
+    the correct syntax for trac roles is :trac:`NUMBER`, note the initial colon
+  pattern: '[^:]trac:`[0-9]'
+
+- name: 'triple_colon: triple colon (::: or : ::)'
+  pattern: ':[ 	]*::$'
+
+# From various typo tickets
+
+# https://github.com/sagemath/sage/issues/30585
+- name: 'typo "homogenous" detected'
+  hint: |
+    in mathematics it should be "homogeneous"
+  pattern: 'homogenous'
+
+# Modularization anti-patterns
+
+- name: 'namespace_pkg_all_import: import from .all of a namespace package'
+  hint: |
+    Sage library code should not import from sage.PAC.KAGE.all when sage.PAC.KAGE is an implicit
+    namespace package. Type import_statements("SOME_IDENTIFIER") to find a more specific import,
+    or use 'sage --fiximports' to fix automatically in the source file.
+  # Keep in sync with SAGE_ROOT/src/sage/misc/replace_dot_all.py
+  pattern: 'from\s+sage(|[.](arith|categories|combinat|crypto|databases|data_structures|dynamics|ext|game_theory|games|graphs|groups|interfaces|manifolds|matrix|matroids|misc|modules|monoids|numerical|probability|quadratic_forms|quivers|rings|sat|schemes|sets|stats|symbolic|tensor)[a-z0-9_.]*|[.]libs)[.]all\s+import'
+  # imports from .all are allowed in all.py; also allow in some modules that need sage.all
+  filePattern: '(.*/|)(?!(all|benchmark|dev_tools|parsing|sage_eval))[^/.]*[.](py|pyx|pxi)$'
+
+# Magic doctest comments
+
+- name: 'multiline_doctest_comment: magic comment on a continuation line'
+  hint: |
+    magic doctest comments should appear on the "sage:" line, not "....:" lines
+  # see optional_regex in src/sage/doctest/parsing.py
+  # "indirect doctest" is from src/bin/sage-coverage
+  pattern: '^[ 	]*[.][.][.][.]:.*#.*(arb216|arb218|py2|py3|long time|not implemented|not tested|known bug|optional|indirect doctest)'

CHANGELOG.md

@@ -2,6 +2,27 @@
 
 All notable changes will be made in this file.
 
+## [0.1.0] - 2024-02-09
+
+### Added
+
+- (#18) Implemented Cocircuits and covectors.
+- (#14) Added some additional examples to ensure tests catch potential errors.
+
+### Changed
+
+- (#22) Updated the documentation to be more complete.
+- (#12) Altered it so that the `to_xxx()` functions are encapsulated in the function `change_type()`.
+- (#2) Updated package to fit into up to date methods for making packages.
+- (#1) Restructed the OrientedMatroids class. In particular:
+    - Removed the category implementation and structured based off the matroid implementation.
+    - There is now an `AbstractOrientedMatroid` class which handles the abstract methods and everything pulls from here.
+
+### Fixed
+
+- (#15) Fixed the groundset error bug.
+
+
 ## [0.0.2] - 2020-12-15
 
 ### Added

Dockerfile

@@ -1,7 +1,7 @@
 # Dockerfile for binder
 # Reference: https://mybinder.readthedocs.io/en/latest/dockerfile.html#preparing-your-dockerfile
 
-FROM sagemath/sagemath:9.2
+FROM sagemath/sagemath:10.0
 
 # Copy the contents of the repo in ${HOME}
 COPY --chown=sage:sage . ${HOME}

MANIFEST.in

@@ -0,0 +1,2 @@
+include README.md
+include VERSION

README.md

@@ -4,27 +4,64 @@ This package contains an oriented matroid implementation for sagemath.
 
 ## Current version
 
-**NOTE:** This package currently does not work. If you would like to help with the development, please let Aram know.
+The current version is 0.1.0 and is compatible/has been tested with sagemath 10.0, 10.1 and 10.2. It is in beta and is open for testing from others.
+
+**NOTE:** This package will be integrating into SageMath directly. If you see any errors while using this please, open an issue and let us know so we can correct it.
 
-The current version is 0.0.2 and is compatible with sagemath 9.2.
 
 ## Installation
 
+### Installation from Pypi
+Use `pip` to install the package:
+
+```
+$ sage -pip install oriented_matroids
+```
+
 ### Local install from source
 Download the source from the git repository:
-
-`$ git clone https://github.com/thecaligarmo/oriented_matroids.git`
+```
+$ git clone https://github.com/thecaligarmo/oriented_matroids.git
+```
 
 Change to the root directory and run:
+```
+$ sage -pip install .
+```
+
+For convenience this package contains a makefile with this and other often used commands. This file neds updating to your sage installation directory before running.
 
-`$ sage -pip install .`
+```
+$ make install
+```
 
-For convenience this package contains a makefile with this and other often used commands. Should you wish too, you can use the shorthand:
+### Common errors
 
-`$ make install`
+1. If you get "SSL" errors, try the fixes found on: [ask sagemath](https://ask.sagemath.org/question/51130/ssl-error-using-sage-pip-install-to-download-a-package/)
+2. If `make` didn't work, make sure you updated where your sage directory is in the make file.
 
-Note that you might need to alter the make file in order for this to run properly if your sage is located in another directory.
 
-### Common errors
+## Using the package after install
+After install, you can start sage and run the following command to have all methods available:
+```
+from oriented_matroids import *
+```
+
+## Uninstall
+To uninstall the package you can run the following command
+```
+$ sage -pip uninstall oriented_matroids
+```
+
+Alternatively, if you installed locally and want to uninstall using `make`, you can run:
+```
+$ make uninstall
+```
+
+## Documentation
+To make the documentation, you can use `make`:
+```
+$ make doc
+```
 
-If you get "SSL" errors, try the fixes found on: [ask sagemath](https://ask.sagemath.org/question/51130/ssl-error-using-sage-pip-install-to-download-a-package/)
+To refresh the doc, I would recommend first cleaning it using `make clean` before running `make doc` again, just in case.

VERSION

@@ -1 +1 @@
-0.0.2
+0.1.0

docs/source/conf.py

@@ -29,8 +29,6 @@
 except ImportError:
     raise RuntimeError("to build the documentation you need to be inside a Sage shell (run first the command 'sage -sh' in a shell")
 
-
-
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
@@ -47,7 +45,8 @@
 # ones.
 extensions = [
     #'sphinx.ext.autodoc',
-    'sage_autodoc',
+    #'sage_autodoc',
+    'sage_docbuild.ext.sage_autodoc',
     'sage_package.sphinx',
     'sphinx.ext.doctest',
     'sphinx.ext.coverage',
@@ -66,8 +65,6 @@
 # The master toctree document.
 master_doc = 'index'
 
-
-
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
@@ -232,7 +229,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-  ('index', package_name + '.tex', u'Documentation of ' + unicode(package_name),
+  ('index', package_name + '.tex', u'Documentation of ' + str(package_name),
    authors, 'manual'),
 ]
 
@@ -262,7 +259,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', package_name, unicode(package_name) + u" documentation",
+    ('index', package_name, str(package_name) + u" documentation",
      [authors], 1)
 ]
 
@@ -276,7 +273,7 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', package_name, unicode(package_name) + u" documentation",
+  ('index', package_name, str(package_name) + u" documentation",
    authors, package_name, project,
    'Miscellaneous'),
 ]
@@ -322,13 +319,14 @@
     exclude_patterns=['**/'+os.path.join(mathjax_relative, i) for i in ('docs', 'README*', 'test',
                                                                         'unpacked', 'LICENSE')]
 else:
-     extensions.append('sphinx.ext.pngmath')
+    extensions.append('sphinx.ext.imgmath')
 
 # This is to make the verbatim font smaller;
 # Verbatim environment is not breaking long lines
 from sphinx.highlighting import PygmentsBridge
 from pygments.formatters.latex import LatexFormatter
 
+
 class CustomLatexFormatter(LatexFormatter):
     def __init__(self, **options):
         super(CustomLatexFormatter, self).__init__(**options)

docs/source/index.rst

@@ -12,7 +12,7 @@ Oriented Matroids
     :maxdepth: 1
 
     oriented_matroids/oriented_matroid
-    oriented_matroids/oriented_matroids_category
+    oriented_matroids/abstract_oriented_matroid
 
 Representations
 ---------------
@@ -22,7 +22,7 @@ Representations
 
     oriented_matroids/circuit_oriented_matroid
     oriented_matroids/covector_oriented_matroid
-    oriented_matroids/hyperplane_arrangement_oriented_matroid
+    oriented_matroids/real_hyperplane_arrangement_oriented_matroid
     oriented_matroids/vector_oriented_matroid
 
 Elements
@@ -32,7 +32,6 @@ Elements
     :maxdepth: 1
 
     oriented_matroids/signed_subset_element
-    oriented_matroids/signed_vector_element
 
 Indices and Tables
 ==================

docs/source/oriented_matroids/oriented_matroids_category.rst → docs/source/oriented_matroids/abstract_oriented_matroid.rst

@@ -1,9 +1,9 @@
 .. nodoctest
 
-Oriented Matroids Category
+Abstract Oriented Matroids
 ==========================
 
-.. automodule:: oriented_matroids.oriented_matroids_category
+.. automodule:: oriented_matroids.abstract_oriented_matroid
     :members:
     :undoc-members:
     :show-inheritance:

docs/source/oriented_matroids/real_hyperplane_arrangement_oriented_matroid.rst

@@ -0,0 +1,9 @@
+.. nodoctest
+
+Real Hyperplane Arrangement Oriented Matroids
+=============================================
+
+.. automodule:: oriented_matroids.real_hyperplane_arrangement_oriented_matroid
+    :members:
+    :undoc-members:
+    :show-inheritance:

makefile

@@ -9,7 +9,7 @@ SAGE = /sage/sage/sage
 all: install test
 
 install:
-	$(SAGE) -pip install --upgrade --no-index -v .
+	$(SAGE) -pip install --upgrade --no-index --no-build-isolation -v .
 
 uninstall:
 	$(SAGE) -pip uninstall $(PACKAGE)

oriented_matroids/__init__.py

@@ -1,7 +1,7 @@
 from __future__ import absolute_import
 from .oriented_matroid import OrientedMatroid
-from .oriented_matroids_category import OrientedMatroids
+from .abstract_oriented_matroid import AbstractOrientedMatroid
 
-from sage.misc.lazy_import import lazy_import
-lazy_import('sage.matroids.oriented_matroids',
-            'oriented_matroids_catalog', 'oriented_matroids')
+# from sage.misc.lazy_import import lazy_import
+# lazy_import('sage.matroids.oriented_matroids',
+#            'oriented_matroids_catalog', 'oriented_matroids')