installer merge requestshttps://git.fmrib.ox.ac.uk/fsl/installer/-/merge_requests2023-01-23T13:42:53+00:00https://git.fmrib.ox.ac.uk/fsl/installer/-/merge_requests/25Mnt/embed manifest2023-01-23T13:42:53+00:00Paul McCarthyMnt/embed manifestEmbed the legacy `manifest.json` file into the legacy installer script. Also fix #6Embed the legacy `manifest.json` file into the legacy installer script. Also fix #6https://git.fmrib.ox.ac.uk/fsl/installer/-/merge_requests/24BF: Make sure FSLDIR is absolue path in profile file2022-05-11T15:47:40+01:00Paul McCarthyBF: Make sure FSLDIR is absolue path in profile fileIn !20, I snuck in a small enhancement, changing the script to accept relative paths when the user is prompted for the destination directory. However, I forgot to make the same change for when the destination directory is specified via t...In !20, I snuck in a small enhancement, changing the script to accept relative paths when the user is prompted for the destination directory. However, I forgot to make the same change for when the destination directory is specified via the command-line interface.https://git.fmrib.ox.ac.uk/fsl/installer/-/merge_requests/23Bf/py3 compat2022-04-30T15:33:12+01:00Paul McCarthyBf/py3 compatA couple of python 2/3-related fixes, and a fix to the handling of default answers to questionaA couple of python 2/3-related fixes, and a fix to the handling of default answers to questionahttps://git.fmrib.ox.ac.uk/fsl/installer/-/merge_requests/22Mnt/linux dist2022-04-21T15:57:27+01:00Paul McCarthyMnt/linux distRefer to:
* https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;c48ae3ba.2110
* https://stackoverflow.com/questions/33996196/why-does-platform-linux-distribution-returns-different-results-on-one-osRefer to:
* https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;c48ae3ba.2110
* https://stackoverflow.com/questions/33996196/why-does-platform-linux-distribution-returns-different-results-on-one-oshttps://git.fmrib.ox.ac.uk/fsl/installer/-/merge_requests/21RF: Don't have separate py2/3 versions - have a single script2022-04-21T12:44:17+01:00Paul McCarthyRF: Don't have separate py2/3 versions - have a single scriptAdapt the installer script to work with any Python version >=2.7. We think that the need to support older versions was for RHEL6 (now out-of-support) and older OSX machines (absolutely now out-of-support).Adapt the installer script to work with any Python version >=2.7. We think that the need to support older versions was for RHEL6 (now out-of-support) and older OSX machines (absolutely now out-of-support).https://git.fmrib.ox.ac.uk/fsl/installer/-/merge_requests/20Mnt/py32022-05-11T15:31:34+01:00Paul McCarthyMnt/py3Port of `fslinstaller.py` to work with python 3.8. Only the default execution pathway has been tested.Port of `fslinstaller.py` to work with python 3.8. Only the default execution pathway has been tested.https://git.fmrib.ox.ac.uk/fsl/installer/-/merge_requests/19Allow a specific FSL build to be installed2021-03-22T17:37:26+00:00Paul McCarthyAllow a specific FSL build to be installed * The `--listversions` output is ordered sensibly
* New `--listbuilds` option to list all available builds for each FSL version
* New `--fslbuild` option to ignore the host environment and download a specific FSL build.
* Added a klu... * The `--listversions` output is ordered sensibly
* New `--listbuilds` option to list all available builds for each FSL version
* New `--fslbuild` option to ignore the host environment and download a specific FSL build.
* Added a kludge so that, if the installer is executed on an Apple M1 system, the x86 FSL version is downloaded.https://git.fmrib.ox.ac.uk/fsl/installer/-/merge_requests/18Re-organise fslinstaller project directory, add tests, run tests with CI2020-12-02T13:33:41+00:00Paul McCarthyRe-organise fslinstaller project directory, add tests, run tests with CIThis MR builds upon !17, but makes a few minor adjustments, and uses CI to automatically run unit tests.
Because `fslinstaller.py` is a stand-alone executable which is never intended to be installed into a python environment or used pro...This MR builds upon !17, but makes a few minor adjustments, and uses CI to automatically run unit tests.
Because `fslinstaller.py` is a stand-alone executable which is never intended to be installed into a python environment or used programmatically, there is no need to have any sort of package structure. So the `fslinstaller.py` script has been moved to the project root, and package files have been removed.
Version number also bumped to 3.0.21https://git.fmrib.ox.ac.uk/fsl/installer/-/merge_requests/17major repo refactoring. Not many changes to actual fslinstaller.py2020-12-02T13:33:41+00:00Taylor Hanayiktaylor.hanayik@ndcn.ox.ac.ukmajor repo refactoring. Not many changes to actual fslinstaller.pychanged testing mechanism to pytest and refactored repo to be organized differently. removed VM directory and made it its own project.changed testing mechanism to pytest and refactored repo to be organized differently. removed VM directory and made it its own project.Taylor Hanayiktaylor.hanayik@ndcn.ox.ac.ukTaylor Hanayiktaylor.hanayik@ndcn.ox.ac.ukhttps://git.fmrib.ox.ac.uk/fsl/installer/-/merge_requests/16add new patch for fsl 6.0.4 asl_gui bug2020-12-01T10:58:11+00:00Taylor Hanayiktaylor.hanayik@ndcn.ox.ac.ukadd new patch for fsl 6.0.4 asl_gui bugproblem:
fsl-6.0.4 asl_gui was shipped with a broken fsleyes preview panel.
People downloading this version if FSL are not able to use the asl_gui.
We need to patch the gui code to fix this error.
Solution:
update the fslinstaller.py ...problem:
fsl-6.0.4 asl_gui was shipped with a broken fsleyes preview panel.
People downloading this version if FSL are not able to use the asl_gui.
We need to patch the gui code to fix this error.
Solution:
update the fslinstaller.py script
- detect if the downloaded FSL version is 6.0.4
- if so, patch $FSLDIR/python/oxford_asl/gui/preview_fsleyes.py
- if any other FSL version do nothing.
Procedure:
- download and install fsl 6.0.4 with the installer script.
- after all files have been moved to the correect locations patch the asl bug in the post install routineDuncan MortimerDuncan Mortimerhttps://git.fmrib.ox.ac.uk/fsl/installer/-/merge_requests/15BF: Handle spaces in filename / destination when installing installer2020-11-06T13:05:27+00:00Paul McCarthyBF: Handle spaces in filename / destination when installing installerFixes this bug: https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;327ee93c.2011
If the `fslinstaller.py` script is downloaded to a location which contains a space, the call-out to `cp` is not quoted correctly.Fixes this bug: https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;327ee93c.2011
If the `fslinstaller.py` script is downloaded to a location which contains a space, the call-out to `cp` is not quoted correctly.Duncan MortimerDuncan Mortimerhttps://git.fmrib.ox.ac.uk/fsl/installer/-/merge_requests/14bump version number2020-09-29T11:17:39+01:00Taylor Hanayiktaylor.hanayik@ndcn.ox.ac.ukbump version numberDuncan MortimerDuncan Mortimerhttps://git.fmrib.ox.ac.uk/fsl/installer/-/merge_requests/13fix t_version to update to parent version (e.g. centos 7) when alias is used2020-09-29T09:32:23+01:00Taylor Hanayiktaylor.hanayik@ndcn.ox.ac.ukfix t_version to update to parent version (e.g. centos 7) when alias is usedDuncan MortimerDuncan Mortimerhttps://git.fmrib.ox.ac.uk/fsl/installer/-/merge_requests/12update installer for AWS linux 2 vendor support2020-09-28T16:35:01+01:00Taylor Hanayiktaylor.hanayik@ndcn.ox.ac.ukupdate installer for AWS linux 2 vendor supportDuncan MortimerDuncan Mortimerhttps://git.fmrib.ox.ac.uk/fsl/installer/-/merge_requests/11RF: Fix matlab startup.m creation2020-09-22T13:52:49+01:00Paul McCarthyRF: Fix matlab startup.m creationThis MR proposes two changes to the default FSL MATLAB configuration:
1. The default MATLAB userpath is `~/Documents/MATLAB/` on both macOS and Linux (https://www.mathworks.com/help/matlab/ref/userpath.html), but the installer creates/e...This MR proposes two changes to the default FSL MATLAB configuration:
1. The default MATLAB userpath is `~/Documents/MATLAB/` on both macOS and Linux (https://www.mathworks.com/help/matlab/ref/userpath.html), but the installer creates/edits `~/matlab/startup.m`.
2. Many FSL commands will not work if the `FSLOUTPUTTYPE` environment variable is not set, so this has been added to the default `startup.m` contentsDuncan MortimerDuncan Mortimerhttps://git.fmrib.ox.ac.uk/fsl/installer/-/merge_requests/10Fix error handling in open_url2019-06-12T10:02:45+01:00Paul McCarthyFix error handling in open_urlhttps://git.fmrib.ox.ac.uk/fsl/installer/-/merge_requests/9Thanayik version fix2019-03-07T13:51:57+00:00Taylor Hanayiktaylor.hanayik@ndcn.ox.ac.ukThanayik version fixSet `Version` to `3.0.14` to fix this from happening:
the installer updates to 3.0.14 but displays that it's running 3.0.13
```
(python2) THMBPr15-19:Downloads thanayik$ python fslinstaller.py
--- FSL Installer - Version 3.0.13 ---
[W...Set `Version` to `3.0.14` to fix this from happening:
the installer updates to 3.0.14 but displays that it's running 3.0.13
```
(python2) THMBPr15-19:Downloads thanayik$ python fslinstaller.py
--- FSL Installer - Version 3.0.13 ---
[Warning] Some operations of the installer require administative rights,
for example installing into the default folder of /usr/local.
If your account is an 'Administrator' (you have 'sudo' rights)
then you will be prompted for your administrator password
when necessary.
When asked a question, the default answer is given in square brackets.
Hit the Enter key to accept this default answer.
There is a newer version (3.0.14) of the installer (you have 3.0.13) updating...
Checking FSL package
--- FSL Installer - Version 3.0.13 ---
[Warning] Some operations of the installer require administative rights,
for example installing into the default folder of /usr/local.
If your account is an 'Administrator' (you have 'sudo' rights)
then you will be prompted for your administrator password
when necessary.
When asked a question, the default answer is given in square brackets.
Hit the Enter key to accept this default answer.
[OK] Installer updated to latest version 3.0.13
[OK] Installer self update successful.
Where would you like the FSL install to be (including the FSL folder name)? [/usr/local/fsl]:
```https://git.fmrib.ox.ac.uk/fsl/installer/-/merge_requests/7fix naked percent sign in matlab shell setup2019-03-07T13:34:04+00:00Taylor Hanayiktaylor.hanayik@ndcn.ox.ac.ukfix naked percent sign in matlab shell setupfixed naked percent symbol in matlab shell setup.
see JISC list threads for reported errors:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1902&L=FSL&D=0&P=194733
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1903&L=FSL&O=D&P=...fixed naked percent symbol in matlab shell setup.
see JISC list threads for reported errors:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1902&L=FSL&D=0&P=194733
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1903&L=FSL&O=D&P=86303https://git.fmrib.ox.ac.uk/fsl/installer/-/merge_requests/6BUG: Matlab flag not passed correctly (reported by Steven Tilley)2019-02-08T15:51:11+00:00Paul McCarthyBUG: Matlab flag not passed correctly (reported by Steven Tilley)https://git.fmrib.ox.ac.uk/fsl/installer/-/merge_requests/5BUG: Many calls to craete_file pass a single string, rather than a list of…2019-01-03T17:28:51+00:00Paul McCarthyBUG: Many calls to craete_file pass a single string, rather than a list of…BUG: Many calls to craete_file pass a single string, rather than a list of lines. Was resulting in generated files containing one character per line.BUG: Many calls to craete_file pass a single string, rather than a list of lines. Was resulting in generated files containing one character per line.Duncan MortimerDuncan Mortimer