Merge pull request #44 from js51/irreps_rewrite

Rewrite irreps for H_n

.gitignore

@@ -143,3 +143,4 @@ _site
 *.gz
 *.tex
 .github/Circular-genome-tools.code-workspace
+cgt/.vscode/settings.json

INSTALL.md

@@ -13,14 +13,6 @@ The basic steps (for Linux) are:
 - `cd` into SageMath and run sage for the first time by executing the `sage` file. Wait for it to finish loading, to the point where you get the sage prompt and can type commands. Exit sage.
 - Run the command `sudo ln -s /path/to/SageMath/sage /usr/local/bin/sage` You can now start SageMath from any directory by typing `sage`.
 
-## Installing repsn
-
-Some functions of Circular-genome-tools require the GAP package repsn to be installed within SageMath. To install repsn inside Sage,
-
-- [Download repsn from this link](https://www.gap-system.org/Packages/repsn.html)
-- Extract the files as explained above.
-- move the directory `repsn-3.1.0` into the directory `SageMath/local/share/gap/pkg`
-
 ## Installing Circular Genome Tools
 
 After completing the above steps, execute the command `sage -pip install cgt`. When you import the package, it will warn you of any missing python packages you might need to install, inclding `scipy`, `matplotlib` and `networkx`.

README.md

@@ -13,4 +13,4 @@ If you would like to contribute to `cgt`, please see [`CONTRIBUTING.md`](CONTRIB
 
 If you use this software in your work, please cite it use the citation function on the github page or see [`CITATION.cff`](CITATION.cff)
 
-**Note:** you will need to at least have Sage version 9.0 installed, and have the GAP package `repsn` installed for the copy of GAP that sits inside Sage. If you aren't sure how to do this, see the installation instructions in [`INSTALL.md`](INSTALL.md).
+**Note:** you will need to at least have Sage version 9.0 installed. If you aren't sure how to do this, see the installation instructions in [`INSTALL.md`](INSTALL.md).

VERSION

@@ -1 +1 @@
-0.2.0
+0.3.1

cgt/__init__.py

@@ -4,9 +4,14 @@
 from sage.all_cmdline import gap
 gigs = 30
 old_command = gap._Expect__command
-s = old_command.index('-o ')
-e = old_command.index(' -', s)
-gap._Expect__command = gap._Expect__command.replace(gap._Expect__command[s:e], f'-o {gigs}G')
+try:
+    s = old_command.index('-o ')
+    e = old_command.index(' -', s)
+    gap._Expect__command = gap._Expect__command.replace(gap._Expect__command[s:e], f'-o {gigs}G')
+except ValueError:
+    s = old_command.index('-b ')
+    e = old_command.index(' -', s)
+    gap._Expect__command = gap._Expect__command.replace(gap._Expect__command[s:e], f'-b -o {gigs}G')
 from .examples import *
 from .enums import *
 from .position_paradigm import PositionParadigmFramework