Initial commit: lalsuite-v7.3

00boot

+#!/bin/sh
+
+## function to print error message and exit
+fail () {
+  echo "!!! $0: $1" >&2
+  exit 1
+}
+
+## check script is being run from top-level source directory
+test "$0" = "./00boot" || fail "must be run from top-level source directory"
+
+## remove M4 cache files
+rm -rf autom4te.cache/
+rm -f aclocal.m4
+
+# FIXME: autoreconf from Ubuntu 9.10 (and probably also from recent
+# Debian versions) automatically run libtoolize with the --copy option
+# therefore over writing the supplied libtool scripts with system
+# version. This can lead to unexpected build failures therefore to work
+# round this "feature" we set the LIBTOOLIZE enviroment variable to
+# point to the the true executable which bypasses the running of
+# libtoolize, this will not effect the vast majority of users and those
+# it will effect will know how to run libtoolize, if required.
+
+## run autoreconf
+AUTORECONF=${AUTORECONF:-"autoreconf"}
+echo "00boot: running ${AUTORECONF}"
+LIBTOOLIZE=true ${AUTORECONF} || fail "${AUTORECONF} failed"
+
+echo "
+==================================================
+00boot has been run successfully.
+Now run './configure' with appropriate options
+to configure LALSuite.
+==================================================
+"

CONTRIBUTING.md

+# Contributing to LALSuite
+
+This page outlines the recommended procedure for contributing changes to the LALSuite repository. Please read the introduction to [GitLab on git.ligo.org](https://wiki.ligo.org/Computing/GitLigoOrg) before you start. 
+
+## Reporting Issues
+
+If you have ligo.org authentication, please report issues directly through gitlab.
+Otherwise, you can use the service desk address
+contact+lscsoft-lalsuite-1438-issue-@support.ligo.org
+to send bug reports by e-mail.
+
+In either case, please include as much detail as possible to reproduce the error, including information about your operating system and the version of each (relevant) component of LALSuite.
+If possible, please include a brief, self-contained code example that demonstrates the problem.
+
+Note that when an issue is marked as 'confidential',
+currently this means that most internal users will also not be able to see it,
+but only a small number of people with reporter, developer or maintainer status.
+
+## Contributing code
+
+All contributions to LALSuite code must be made using the fork and [merge request](https://git.ligo.org/help/user/project/merge_requests/index.md) [workflow](https://git.ligo.org/help/user/project/repository/forking_workflow.md), which must then be reviewed by one of the project maintainers.
+
+If you wish to contribute new code, or changes to existing code, please follow this development workflow:
+
+### Make a fork (copy) of LALSuite
+
+**You only need to do this once**
+
+1. Go to the [LALSuite repository home page](https://git.ligo.org/lscsoft/lalsuite)
+2. Click on the *Fork* button, that should lead you [here](https://git.ligo.org/lscsoft/lalsuite/-/forks/new)
+3. Select the namespace that you want to create the fork in, this will usually be your personal namespace
+
+If you can't see the *Fork* button, make sure that you are logged in by checking for your account profile photo in the top right-hand corner of the screen.
+
+### Clone your fork
+
+Make sure that you have installed and configured [git-lfs](https://wiki.ligo.org/Computing/GitLFS#Install_the_git_LFS_client):
+
+ ```bash
+ git lfs install
+ ```
+
+for the management of large files. This is required to successfully build and install your development fork. 
+
+Then, clone your fork with 
+
+```bash
+git clone git@git.ligo.org:<namespace>/lalsuite.git
+```
+
+### Keeping your fork up to date
+
+Link your clone to the main (`upstream`) repository so that you can `fetch` and `pull` changes, `merge` them with your clone, and `push` them to your fork. Do *not* make changes on your master branch. 
+
+1. Link your fork to the main repository:
+
+    ```bash
+    cd lalsuite
+    git remote add upstream git@git.ligo.org:lscsoft/lalsuite.git
+    ```
+
+   You need only do this step once. 
+
+2. Update your `master` branch to track changes from upstream:
+
+    ```bash
+    git checkout master
+    git fetch upstream
+    git branch --set-upstream-to upstream/master
+    git pull
+    ```
+
+   You only need to do this step once. 
+
+3. Fetch new changes from the `upstream` repository, merge them with your master branch, and push them to your fork on git.ligo.org:
+
+    ```bash
+    git checkout master
+    git pull
+    git push origin master
+    ```
+
+4. You can see which remotes are configured using
+
+   ```bash
+   git remote -v
+   ```
+
+   If you have followed the instructions thus far, you should see four lines. Lines one and two begin with `origin` and reference your fork on git.ligo.org with both `fetch` and `push` methods. Lines three and four begin with `upstream` and refer to the main repository on git.ligo.org with both `fetch` and `push` methods.
+
+### Making changes
+
+All changes should be developed on a feature branch in order to keep them separate from other work, thus simplifying the review and merge once the work is complete. The workflow is:
+
+1. Create a new feature branch configured to track the `master` branch:
+
+   ```bash
+   git checkout master
+   git pull
+   git checkout -b my-new-feature upstream/master
+   ```
+
+   This command creates the new branch `my-new-feature`, sets up tracking the `upstream` repository, and checks out the new branch. There are other ways to do these steps, but this is a good habit since it will allow you to `fetch` and `merge` changes from `upstream/master` directly onto the branch. 
+
+2. Develop the changes you would like to introduce, using `git commit` to finalise a specific change.
+   Ideally commit small units of change often, rather than creating one large commit at the end, this will simplify review and make modifying any changes easier.
+
+   Commit messages should be clear, identifying which code was changed, and why.
+   Common practice is to use a short summary line (<50 characters), followed by a blank line, then more information in longer lines.
+
+2. Push your changes to the remote copy of your fork on https://git.ligo.org.
+   The first `push` of any new feature branch will require the `-u/--set-upstream` option to `push` to create a link between your new branch and the `origin` remote:
+
+    ```bash
+    git push --set-upstream origin my-new-feature
+    ```
+
+    Subsequenct pushes can be made with just:
+
+    ```bash
+    git push
+    ```
+   
+3. Keep your feature branch up to date with the `upstream` repository by doing:
+
+   ```bash
+   git checkout master
+   git pull
+   git checkout my-new-feature
+   git rebase upstream/master
+   git push -f origin my-new-feature
+   ```
+
+   This works if you created your branch with the `checkout` command above. If you forgot to add the `upstream/master` starting point, then you will need to dig deeper into git commands to get changes and merge them into your feature branch. 
+
+   If there are conflicts between `upstream` changes and your changes, you will need to resolve them before pushing everything to your fork. 
+
+### Open a merge request
+
+When you feel that your work is finished, you should create a merge request to propose that your changes be merged into the main (`upstream`) repository.
+
+After you have pushed your new feature branch to `origin`, you should find a new button on the [LALSuite repository home page](https://git.ligo.org/lscsoft/lalsuite/) inviting you to create a merge request out of your newly pushed branch. (If the button does not exist, you can initiate a merge request by going to the `Merge Requests` tab on your fork website on git.ligo.org and clicking `New merge request`)
+
+You should click the button, and proceed to fill in the title and description boxes on the merge request page.
+It is recommended that you check the box to `Remove source branch when merge request is accepted`; this will result in the branch being automatically removed from your fork when the merge request is accepted. 
+
+Once the request has been opened, one of the maintainers will assign someone to review the change. There may be suggestions and/or discussion with the reviewer. These interactions are intended to make the resulting changes better. The reviewer will merge your request.
+
+Once the changes are merged into the upstream repository, you should remove the development branch from your clone using 
+
+```bash
+git branch -d my-new-feature
+```
+
+A feature branch should *not* be repurposed for further development as this can result in problems merging upstream changes. 
+
+### Speeding up the continuous integration pipeline
+
+The Gitlab-CI (continuous integration) pipeline runs for all changes to ensure that the software still builds and passes all of the tests.
+The full pipeline (and even more so the nightly pipeline) takes a long time to carefully go through all of the package builds, but for minor changes to documentation or infrastructure this can be a waste of time and resources.
+
+Sections of the CI pipeline can be skipped by adding special key text to your commit messages as follows:
+
+| Commit message text  | Action                                        |
+| -------------------- | --------------------------------------------- |
+| `[skip compiler]`    | Skip compiler test jobs                       |
+| `[skip conda]`       | Skip Conda build jobs (and their dependents)  |
+| `[skip coverage]`    | Skip coverage jobs                            |
+| `[skip debian]`      | Skip Debian build jobs (and their dependents) |
+| `[skip docs]`        | Skip documentation jobs                       |
+| `[skip integration]` | Skip integration test jobs                    |
+| `[skip lint]`        | Skip lint jobs                                |
+| `[skip platform]`    | Skip platform test jobs                       |
+| `[skip rhel]`        | Skip RHEL build jobs (and their dependents)   |
+| `[skip wheels]`      | Skip Python wheel build jobs test jobs        |
+
+**It is important that this feature is not abused, please do not skip any jobs when making library changes.**
+
+## More Information
+
+More information regarding the usage of GitLab can be found in the main GitLab [documentation](https://git.ligo.org/help/).

COPYING

+                    GNU GENERAL PUBLIC LICENSE
+                       Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users.  This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it.  (Some other Free Software Foundation software is covered by
+the GNU Lesser General Public License instead.)  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
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+this service if you wish), that you receive source code or can get it
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+These restrictions translate to certain responsibilities for you if you
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+
+  For example, if you distribute copies of such a program, whether
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+source code.  And you must show them these terms so they know their
+rights.
+
+  We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
+distribute and/or modify the software.
+
+  Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
+software.  If the software is modified by someone else and passed on, we
+want its recipients to know that what they have is not the original, so
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+  Finally, any free program is threatened constantly by software
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+   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+  0. This License applies to any program or other work which contains
+a notice placed by the copyright holder saying it may be distributed
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+language.  (Hereinafter, translation is included without limitation in
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+Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope.  The act of
+running the Program is not restricted, and the output from the Program
+is covered only if its contents constitute a work based on the
+Program (independent of having been made by running the Program).
+Whether that is true depends on what the Program does.
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+  1. You may copy and distribute verbatim copies of the Program's
+source code as you receive it, in any medium, provided that you
+conspicuously and appropriately publish on each copy an appropriate
+copyright notice and disclaimer of warranty; keep intact all the
+notices that refer to this License and to the absence of any warranty;
+and give any other recipients of the Program a copy of this License
+along with the Program.
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+You may charge a fee for the physical act of transferring a copy, and
+you may at your option offer warranty protection in exchange for a fee.
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+  2. You may modify your copy or copies of the Program or any portion
+of it, thus forming a work based on the Program, and copy and
+distribute such modifications or work under the terms of Section 1
+above, provided that you also meet all of these conditions:
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+    b) You must cause any work that you distribute or publish, that in
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+    part thereof, to be licensed as a whole at no charge to all third
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+    when run, you must cause it, when started running for such
+    interactive use in the most ordinary way, to print or display an
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+    notice that there is no warranty (or else, saying that you provide
+    a warranty) and that users may redistribute the program under
+    these conditions, and telling the user how to view a copy of this
+    License.  (Exception: if the Program itself is interactive but
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+These requirements apply to the modified work as a whole.  If
+identifiable sections of that work are not derived from the Program,
+and can be reasonably considered independent and separate works in
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+distribute the same sections as part of a whole which is a work based
+on the Program, the distribution of the whole must be on the terms of
+this License, whose permissions for other licensees extend to the
+entire whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to
+exercise the right to control the distribution of derivative or
+collective works based on the Program.
+
+In addition, mere aggregation of another work not based on the Program
+with the Program (or with a work based on the Program) on a volume of
+a storage or distribution medium does not bring the other work under
+the scope of this License.
+
+  3. You may copy and distribute the Program (or a work based on it,
+under Section 2) in object code or executable form under the terms of
+Sections 1 and 2 above provided that you also do one of the following:
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+    a) Accompany it with the complete corresponding machine-readable
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+    an offer, in accord with Subsection b above.)
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+If distribution of executable or object code is made by offering
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+distribution of the source code, even though third parties are not
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+
+  4. You may not copy, modify, sublicense, or distribute the Program
+except as expressly provided under this License.  Any attempt
+otherwise to copy, modify, sublicense or distribute the Program is
+void, and will automatically terminate your rights under this License.
+However, parties who have received copies, or rights, from you under
+this License will not have their licenses terminated so long as such
+parties remain in full compliance.
+
+  5. You are not required to accept this License, since you have not
+signed it.  However, nothing else grants you permission to modify or
+distribute the Program or its derivative works.  These actions are
+prohibited by law if you do not accept this License.  Therefore, by
+modifying or distributing the Program (or any work based on the
+Program), you indicate your acceptance of this License to do so, and
+all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+  6. Each time you redistribute the Program (or any work based on the
+Program), the recipient automatically receives a license from the
+original licensor to copy, distribute or modify the Program subject to
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+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
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+distribute so as to satisfy simultaneously your obligations under this
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+may not distribute the Program at all.  For example, if a patent
+license would not permit royalty-free redistribution of the Program by
+all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under
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+
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+This section is intended to make thoroughly clear what is believed to
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+
+  8. If the distribution and/or use of the Program is restricted in
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+countries not thus excluded.  In such case, this License incorporates
+the limitation as if written in the body of this License.
+
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+address new problems or concerns.
+
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+later version", you have the option of following the terms and conditions
+either of that version or of any later version published by the Free
+Software Foundation.  If the Program does not specify a version number of
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+Foundation.
+
+  10. If you wish to incorporate parts of the Program into other free
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+
+                            NO WARRANTY
+
+  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
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+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
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+  To do so, attach the following notices to the program.  It is safest
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+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
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+    This program is free software; you can redistribute it and/or modify
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+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
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+
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+    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
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+
+    Gnomovision version 69, Copyright (C) year name of author
+    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, the commands you use may
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+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary.  Here is a sample; alter the names:
+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+  `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+  <signature of Ty Coon>, 1 April 1989
+  Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs.  If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.

Makefile.am

+BUILT_SOURCES =
+sysconf_DATA =
+MOSTLYCLEANFILES =
+EXTRA_DIST =
+include $(top_srcdir)/gnuscripts/lalsuite_top.am
+
+ACLOCAL_AMFLAGS = -I gnuscripts
+
+SUBDIRS = @subdirs@ wheel
+
+.PHONY: wheel
+wheel:
+	$(MAKE) -C wheel wheel
+
+# Override automake's default rule for rebuilding aclocal.m4, to ensure that
+# ./configure is successfully recreated after certain build system changes which
+# require other autotools (e.g. autoheader) to be re-run. See Redmine issue #728.
+$(lalsuite_package_configure_deps):
+$(ACLOCAL_M4): $(am__aclocal_m4_deps) $(lalsuite_package_configure_deps)
+	$(am__cd) $(srcdir) && $(SHELL) ./00boot
+
+# Override automake's default rule for rebuilding ./config.status, to ensure that
+# all changes to the top-level configuration (especially to environment variables it
+# exports) are propagated to the library-level configurations. See Redmine issue #728.
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+	$(SHELL) $(top_srcdir)/configure $(ac_configure_args)
+
+.PHONY: cscopelist-subdirs
+cscopelist-am: cscopelist-subdirs
+cscopelist-subdirs:
+	for subdir in @subdirs@; do \
+		sed "s|^|$${subdir}/|" $${subdir}/cscope.files >> $(top_builddir)/cscope.files; \
+	done
+
+user_environment = \
+	`for dir in @subdirs@; do printf 'source %s; ' "$(sysconfdir)/$${dir}-user-env"; done` \
+	$(END_OF_LIST)
+
+BUILT_SOURCES += $(PACKAGE)rc
+sysconf_DATA += $(PACKAGE)rc
+MOSTLYCLEANFILES += $(PACKAGE)rc
+$(PACKAGE)rc: Makefile
+	$(AM_V_GEN)echo "# source this file to access $(PACKAGE_NAME) from Bourne or C shells" >$@; \
+	echo "expr \"X\$$0\" : '^X.*csh' >/dev/null && source $(sysconfdir)/$(PACKAGE)-user-env.csh || . $(sysconfdir)/$(PACKAGE)-user-env.sh" >>$@
+
+if DOXYGEN
+
+html-local: Makefile $(CONFIG_CLEAN_FILES)
+	$(AM_V_at)set -e; \
+	echo "$(subdir)/Makefile: Doxygen documentation was built successfully!"; \
+	echo "$(subdir)/Makefile: $(PACKAGE_NAME) main page is at file://$(abs_builddir)/index.html"
+
+install-html-local: html-local
+	$(AM_V_at)set -e; \
+	echo " $(MKDIR_P) '$(DESTDIR)$(htmldir)'"; \
+	$(MKDIR_P) "$(DESTDIR)$(htmldir)"; \
+	echo " $(INSTALL_DATA) index.html '$(DESTDIR)$(htmldir)/index.html'"; \
+	$(SED) -e 's|\(lal[a-z]*\)/doxygen/out|../\1|g' index.html > $@.tmp; \
+	$(INSTALL_DATA) $@.tmp "$(DESTDIR)$(htmldir)/index.html"; \
+	rm -f $@.tmp; \
+	echo "$(subdir)/Makefile: Doxygen documentation was installed successfully!"; \
+	echo "$(subdir)/Makefile: installed $(PACKAGE_NAME) main page is at file://$(DESTDIR)$(htmldir)/index.html"
+
+uninstall-local:
+	-rm -rf "$(DESTDIR)$(htmldir)/"
+
+endif

README.md

+# LALSuite
+
+This is the main LALSuite development repository.
+If you would like to just use a released version,
+see [here](https://computing.docs.ligo.org/conda/)
+for IGWN conda environments including LALSuite,
+or the project pages
+on [conda-forge](https://anaconda.org/conda-forge/lalsuite)
+and on [PyPI](https://pypi.org/project/lalsuite/).
+
+## Acknowledgment
+
+We request that any academic report, publication, or other academic
+disclosure of results derived from the use of this software acknowledge
+the use of the software by an appropriate acknowledgment or citation.
+
+The whole LALSuite software suite can be cited with the DOI
+[10.7935/GT1W-FZ16][doi]. An example BibTeX entry could look like this:
+
+     @misc{lalsuite,
+           author         = "{LIGO Scientific Collaboration}",
+           title          = "{LIGO} {A}lgorithm {L}ibrary - {LALS}uite",
+           howpublished   = "free software (GPL)",
+           doi            = "10.7935/GT1W-FZ16",
+           year           = "2018"
+     }
+
+In addition, some codes contained in this package may be directly based
+on one or several scientific papers, which should be cited when using
+those specific codes; some of these can be discovered through the
+documentation.
+
+## Cloning the Repository
+
+We now utilize [Git LFS][gitlfs] for the managament of large files and
+as such `git-lfs` needs to be installed and configured to correctly
+clone this repository. After installing `git-lfs` it can be configured
+using:
+
+     $ git lfs install
+
+This only needs to be done once for each machine you access the
+repository. It can then be cloned using:
+
+     $ git clone git@git.ligo.org:lscsoft/lalsuite.git
+
+## Building from Source
+
+The recommended way to build LALSuite from source is in a `conda` environment.
+[A recipe file](conda/environment.yml) is available with all main dependencies.
+This can serve as the base for custom recipes,
+or be used directly via:
+
+     $ conda env create -f conda/environment.yml
+
+Pulling in dependencies may take a while depending on your internet connection.
+After the environment setup succeeded, you can activate it with:
+
+     $ conda activate lalsuite-dev
+
+You can then build the suite by executing, in order:
+1. `./00boot` (once at first time)
+2. `./configure` with appropriate options (see `./configure --help`)
+3. `make`
+
+After pulling updates or making your own changes,
+you will usually only need to call `make` again,
+as reconfiguration and re-running `00boot` should be handled automatically if needed.
+
+If you prefer managing dependencies yourself without conda,
+see [here](https://wiki.ligo.org/Computing/LALSuite#Dependencies).
+
+## Contributing to LALSuite
+
+The [guide to contributing to LALSuite][contributing] explains how to
+report issues and contribute fixes or new features using the fork and
+pull workflow. Please read and follow these directions.
+
+## Nightly Documentation
+
+The [LALSuite Doxygen documentation][nightlydocs] is built under
+GitLab-CI every night.
+
+## Notes on Ancient History
+
+LALSuite was transferred to `git.ligo.org` in December 2017. Older
+history has been imported, though commit hashes were rewritten during
+the [Git LFS][gitlfs] conversion. Please note:
+
+1. The `Original:` commit IDs quoted in each commit message can be used
+   to compare with the [archived reference repo][oldlalsuite], old issue
+   discussions on the [Redmine tracker][oldredmine], review wiki pages
+   etc.
+
+1. Commits before December 2017 may also include references to issues
+   (`#number`). These refer to the corresponding [Redmine
+   issue][oldredmine] (LVC-authorized access only), and any clickable
+   link the internal GitLab web interface produces for those old commits
+   will therefore be spurious.
+
+## For More Information
+
+Please visit the [LALSuite project page][project].
+
+[doi]:          https://doi.org/10.7935/GT1W-FZ16
+[gitlfs]:       https://wiki.ligo.org/Computing/GitLFS#Install_the_git_LFS_client
+[contributing]: https://git.ligo.org/lscsoft/lalsuite/blob/master/CONTRIBUTING.md
+[nightlydocs]:  https://lscsoft.docs.ligo.org/lalsuite
+[oldlalsuite]:  https://git.ligo.org/lscsoft/lalsuite-archive
+[oldredmine]:   https://bugs.ligo.org/redmine/projects/lalsuite
+[project]:      https://wiki.ligo.org/Computing/LALSuite

RELEASE.md

+# How to create a LALSuite release
+
+The document attempts to describe the workflow for creating a release of
+a subpackage of LALSuite.
+Note that only authorised persons will be able to push directly to the
+relevant release branch.
+
+The workflow is (roughly) as follows:
+
+1. cherry-pick/merge everything required onto the release branch
+   (e.g. `o3b-release`) via a Merge Request; please use the `-x` and `--gpg-sign`
+   option to `git-cherry-pick`
+1. for each subpackage (e.g. `lal`):
+   1. update the following for the release:
+      - `/lal/configure.ac` (package and library version numbers, and
+        upstream LALSuite dependencies -- carefully read the instructions on
+        how to change the library version number)
+      - `/lal/debian/control.in` (changelog entry)
+      - `/lal/lalsimulation.spec.in` (changelog entry)
+   1. commit the resulting changes onto the release branch
+      (one file at a time, if you like)
+   1. tag `lal-vX.Y.Z` on the release branch
+      ```console
+      git tag --annotate --sign lal-vX.Y.Z
+      ```
+   1. generate the release tarball
+      ```console
+      git checkout lal-vX.Y.Z
+      ./00boot
+      ./configure --enable-swig
+      make dist -C lal
+      git checkout <release-branch>
+      ```
+1. update the following for the top-level `lalsuite` release:
+   - `/configure.ac` (lalsuite version number)
+1. commit the resulting changes onto the release branch
+1. tag `lalsuite-vX.Y` on the release branch
+   ```
+   git tag --annotate --sign lalsuite-vX.Y
+   ```
+1. push the new references up to the repository
+   ```console
+   git push upstream lal-vX.Y.Z  # (repeat as required for each subpackage)
+   git push upstream lalsuite-vX.Y
+   ```
+1. upload the release tarballs to <http://software.ligo.org/lscsoft/source/>
+1. [open an SCCB ticket](https://sccb.docs.ligo.org/requests/)
+1. merge the release branch onto `master` via a Merge Request
+   - use a local branch on your fork to merge the two branches
+   - update the package versions in `/configure.ac` and all
+     `/<subpackage>/configure.ac` files for released subpackages to
+     `X.Y.Z.1` to indicate that they are back in development mode

conda/environment.yml

+name: lalsuite-dev
+channels:
+  - conda-forge
+dependencies:
+  - astropy >=1.1.1
+  - autoconf
+  - automake
+  - bc
+  - cfitsio
+  - doxygen
+  - fftw
+  - freezegun
+  - c-compiler
+  - gsl
+  - h5py
+  - hdf5
+  - healpy
+  - help2man >=1.37
+  - ldas-tools-framecpp
+  - libframel
+  - ligo-gracedb
+  - ligo-segments
+  - lscsoft-glue >=2.0.0
+  - make
+  - matplotlib-base
+  - metaio
+  - mpmath >=1.0.0
+  - numpy
+  - openmpi
+  - pillow
+  - pkg-config >=0.18.0
+  - pytest
+  - python
+  #- python-ligo-lw  <-- depends upon python-lal
+  - scipy >=0.9.0
+  - six
+  - swig >=3.0.10
+  - texlive-core
+  - zlib

conda/install-bin.sh

+#!/bin/bash
+
+set -ex
+
+# install from python build directory
+_pybuilddir="_build${PY_VER}"
+cd ${_pybuilddir}
+
+# install binaries
+make -j ${CPU_COUNT} V=1 VERBOSE=1 install -C bin
+
+# install system configuration files
+make -j ${CPU_COUNT} V=1 VERBOSE=1 install-sysconfDATA

conda/install-lib.sh

+#!/bin/bash
+
+set -ex
+
+cd _build
+
+# install library and headers
+make -j ${CPU_COUNT} V=1 VERBOSE=1 -C lib install
+
+# install SWIG binding definitions and headers
+make -j ${CPU_COUNT} V=1 VERBOSE=1 -C swig install-data
+
+# install pkg-config
+make -j ${CPU_COUNT} V=1 VERBOSE=1 install-pkgconfigDATA
+
+# -- create activate/deactivate scripts
+
+# strip out the 'lib' package name prefix
+LALSUITE_NAME=${PKG_NAME#"lib"}
+LALSUITE_NAME_UPPER=$(echo ${LALSUITE_NAME} | awk '{ print toupper($0) }')
+
+# activate.sh
+ACTIVATE_SH="${PREFIX}/etc/conda/activate.d/activate-${PKG_NAME}.sh"
+mkdir -p $(dirname ${ACTIVATE_SH})
+cat > ${ACTIVATE_SH} << EOF
+#!/bin/bash
+
+# preserve user setting
+if [ ! -z "\"{${LALSUITE_NAME_UPPER}_DATADIR+x}" ]; then
+	export CONDA_BACKUP_${LALSUITE_NAME_UPPER}_DATADIR="\${${LALSUITE_NAME_UPPER}_DATADIR}"
+fi
+
+export ${LALSUITE_NAME_UPPER}_DATADIR="\${CONDA_PREFIX}/share/${LALSUITE_NAME}"
+EOF
+
+# deactivate.sh
+DEACTIVATE_SH="${PREFIX}/etc/conda/deactivate.d/deactivate-${PKG_NAME}.sh"
+mkdir -p $(dirname ${DEACTIVATE_SH})
+cat > ${DEACTIVATE_SH} << EOF
+#!/bin/bash
+
+# reinstate backup from outside the environment
+if [ ! -z "\${CONDA_BACKUP_LAL_DATADIR}" ]; then
+	export ${LALSUITE_NAME_UPPER}_DATADIR="\${CONDA_BACKUP_${LALSUITE_NAME_UPPER}_DATADIR}"
+	unset CONDA_BACKUP_${LALSUITE_NAME_UPPER}_DATADIR
+# no backup, just unset
+else
+	unset ${LALSUITE_NAME_UPPER}_DATADIR
+fi
+EOF

configure.ac

+AC_PREREQ([2.63])
+AC_INIT([LALSuite],[7.3],[lal-discuss@ligo.org])
+AC_CONFIG_SRCDIR([configure.ac])
+AC_CONFIG_AUX_DIR([gnuscripts])
+AC_CONFIG_MACRO_DIR([gnuscripts])
+AC_PREFIX_DEFAULT(["`pwd`/_inst"])
+AC_CONFIG_FILES([Makefile wheel/Makefile wheel/setup.py])
+AM_INIT_AUTOMAKE([ \
+  1.11 \
+  foreign \
+  subdir-objects \
+  color-tests \
+  parallel-tests \
+  tar-pax \
+  dist-xz \
+  no-dist-gzip \
+])
+
+LALSUITE_DISTCHECK_CONFIGURE_FLAGS
+
+# use silent build rules
+AM_SILENT_RULES([yes])
+
+# check for programs
+AC_PROG_AWK
+AC_PROG_SED
+
+LALSUITE_ENABLE_NIGHTLY
+LALSUITE_CHECK_PYTHON([3.5])
+
+# provide LAL library enable/disable options
+LALSUITE_ENABLE_ALL_LAL
+lal=true
+LALSUITE_ENABLE_LALFRAME
+LALSUITE_ENABLE_LALMETAIO
+LALSUITE_ENABLE_LALSIMULATION
+LALSUITE_ENABLE_LALBURST
+LALSUITE_ENABLE_LALINSPIRAL
+LALSUITE_ENABLE_LALPULSAR
+LALSUITE_ENABLE_LALINFERENCE
+LALSUITE_ENABLE_LALAPPS
+
+# configure Doxygen top-level page
+LALSUITE_ENABLE_DOXYGEN
+LALSUITE_ENABLE_MODULE([DOXYGEN])
+AS_IF([test "x${doxygen}" = xtrue],[
+  AC_CONFIG_FILES([index.html:gnuscripts/lalsuite_index.html.in])
+  AC_SUBST([DOXYGEN_PACKAGE_LINKS],[])
+  AM_SUBST_NOTMAKE([DOXYGEN_PACKAGE_LINKS])
+  AC_SUBST([DOXYGEN_LAST_PACKAGE],[])
+  AM_SUBST_NOTMAKE([DOXYGEN_LAST_PACKAGE])
+])
+AC_DEFUN([lalsuite_config_doxygen],[
+  m4_pushdef([lowercase],m4_translit([[$1]], [A-Z], [a-z]))
+  AS_IF([test "x${doxygen}" = xtrue],[
+    DOXYGEN_PACKAGE_LINKS="${DOXYGEN_PACKAGE_LINKS}"' <a target="docframe" href="lowercase/doxygen/out/index.html">$1</a>'
+    DOXYGEN_LAST_PACKAGE="lowercase/doxygen/out/index.html"
+  ])
+  m4_popdef([lowercase])
+])
+
+# directories of top-level build and source
+lalsuite_abs_top_builddir="`pwd`"
+lalsuite_abs_top_srcdir='$(abs_top_srcdir)/..'
+
+# configure a lalsuite package
+AC_DEFUN([lalsuite_config_subdir],[
+  m4_pushdef([lowercase],m4_translit([[$1]], [A-Z], [a-z]))
+  m4_pushdef([uppercase],m4_translit([[$1]], [a-z], [A-Z]))
+
+  # if $1 is enabled
+  AS_IF([test "x${lowercase}" = xtrue],[
+
+    # re-run top-level ./00boot if any package-level ./configure.ac have changed
+    # - this is needed to pick up e.g. any new inter-package dependencies
+    lalsuite_package_configure_deps="${lalsuite_package_configure_deps} "'$(top_srcdir)/lowercase/configure.ac'
+
+    # export precious environment variables
+    uppercase[]_LIBS="${lalsuite_abs_top_builddir}/lowercase/lib/lib[]lowercase.la"
+    uppercase[]_CFLAGS="-I${lalsuite_abs_top_builddir}/lowercase/include"
+    uppercase[]_DATA_PATH="${lalsuite_abs_top_srcdir}/lowercase/lib:${lalsuite_abs_top_srcdir}/lowercase/test"
+    uppercase[]_OCTAVE_PATH="${lalsuite_abs_top_builddir}/lowercase/octave"
+    uppercase[]_PYTHON_PATH="${lalsuite_abs_top_builddir}/lowercase/python"
+    uppercase[]_HTMLDIR="${htmldir}/../lowercase"
+    export uppercase[]_LIBS uppercase[]_CFLAGS uppercase[]_HTMLDIR
+    export uppercase[]_DATA_PATH uppercase[]_OCTAVE_PATH uppercase[]_PYTHON_PATH
+
+    # configure Doxygen top-level page
+    lalsuite_config_doxygen([$1])
+
+    # configure $1
+    AC_CONFIG_SUBDIRS(lowercase)
+
+    # set enable string
+    uppercase[]_ENABLE_VAL=ENABLED
+  ],[
+    # set disable string
+    uppercase[]_ENABLE_VAL=DISABLED
+  ])
+
+  m4_popdef([lowercase])
+  m4_popdef([uppercase])
+])
+
+# lal and lalsupport are always configured
+lalsuite_config_doxygen([LAL])
+AC_CONFIG_SUBDIRS(lal)
+lalsuite_package_configure_deps='$(top_srcdir)/lal/configure.ac'
+LAL_LIBS="${lalsuite_abs_top_builddir}/lal/lib/liblal.la"
+LAL_CFLAGS="-I${lalsuite_abs_top_builddir}/lal/include"
+LAL_DATA_PATH="${lalsuite_abs_top_srcdir}/lal/test"
+LAL_OCTAVE_PATH="${lalsuite_abs_top_builddir}/lal/octave"
+LAL_PYTHON_PATH="${lalsuite_abs_top_builddir}/lal/python"
+LAL_HTMLDIR="${htmldir}/../lal"
+LALSUPPORT_LIBS="${lalsuite_abs_top_builddir}/lal/lib/support/liblalsupport.la"
+LALSUPPORT_CFLAGS="-I${lalsuite_abs_top_builddir}/lal/include"
+LALSUPPORT_DATA_PATH="${LAL_DATA_PATH}"
+LALSUPPORT_OCTAVE_PATH="${LAL_OCTAVE_PATH}"
+LALSUPPORT_PYTHON_PATH="${LAL_PYTHON_PATH}"
+LALSUPPORT_HTMLDIR="${htmldir}/../lal"
+LALSUITE_BUILD="true"
+export LALSUITE_BUILD
+export LAL_LIBS LAL_CFLAGS LAL_DATA_PATH LAL_OCTAVE_PATH LAL_PYTHON_PATH LAL_HTMLDIR
+export LALSUPPORT_LIBS LALSUPPORT_CFLAGS LALSUPPORT_DATA_PATH LALSUPPORT_OCTAVE_PATH LALSUPPORT_PYTHON_PATH LALSUPPORT_HTMLDIR
+
+# configure optional packages
+lalsuite_config_subdir([LALFrame])
+lalsuite_config_subdir([LALMetaIO])
+lalsuite_config_subdir([LALSimulation])
+lalsuite_config_subdir([LALBurst])
+lalsuite_config_subdir([LALInspiral])
+lalsuite_config_subdir([LALPulsar])
+lalsuite_config_subdir([LALInference])
+
+# optionally configure lalapps
+AS_IF([test "x$lalapps" = xtrue],[
+  lalsuite_package_configure_deps="${lalsuite_package_configure_deps} "'$(top_srcdir)/lalapps/configure.ac'
+  lalsuite_config_doxygen([LALApps])
+  AC_CONFIG_SUBDIRS(lalapps)
+  LALAPPS_ENABLE_VAL=ENABLED
+],[
+  LALAPPS_ENABLE_VAL=DISABLED
+])
+
+AC_SUBST([ac_configure_args])
+AC_SUBST([lalsuite_package_configure_deps])
+AC_OUTPUT
+AC_MSG_NOTICE([
+==================================================
+LALSuite has now been successfully configured:
+
+* LALFrame library support is $LALFRAME_ENABLE_VAL
+* LALMetaIO library support is $LALMETAIO_ENABLE_VAL
+* LALSimulation library support is $LALSIMULATION_ENABLE_VAL
+* LALBurst library support is $LALBURST_ENABLE_VAL
+* LALInspiral library support is $LALINSPIRAL_ENABLE_VAL
+* LALPulsar library support is $LALPULSAR_ENABLE_VAL
+* LALInference library support is $LALINFERENCE_ENABLE_VAL
+* LALApps library support is $LALAPPS_ENABLE_VAL
+* Doxygen documentation is $DOXYGEN_ENABLE_VAL
+
+and will be installed under the directory:
+
+${prefix}
+
+Now run 'make' to build LALSuite,
+and run 'make install' to install LALSuite.
+==================================================
+])

docker/startup

+#!/bin/sh
+
+# use entrypoint structure so that we can do more at startup in the future, such as ligo-proxy-init
+
+#if ! grid-proxy-info -exists -valid 1:0 2>/dev/null; then
+#  read -p "Enter your LIGO.ORG username: " username && echo $username | xargs -n 1 ligo-proxy-init
+#fi
+
+exec "$@"

doxygen/README.md

+# LALSuite Doxygen documentation
+
+Online HTML documentation for the LALSuite C libraries and Pure-python extras
+is generated using [Doxygen](http://www.doxygen.nl/).
+
+This directory (`/doxygen/`) contains the common files that are shared between
+the doxygen builds for all of the LALSuite subpackages.
+
+The build is controlled by the automake file `/gnuscripts/lalsuite_doxygen.am`,
+customisations for each subpackage can be added in
+`<package>/doxygen/Makefile.am`.

doxygen/check_tags.py

+# check_tags.py - check Doxygen tags
+
+__author__ = 'Karl Wette <karl.wette@ligo.org>'
+__copyright__ = 'Copyright (C) 2015 Karl Wette'
+
+import sys
+from xml.etree.cElementTree import ElementTree
+
+# print error message and exit
+def fail(msg):
+    sys.stderr.write('%s: %s\n' % (sys.argv[0], msg))
+    sys.exit(1)
+
+# get input arguments
+tagfile, = sys.argv[1:]
+
+# parse tag file
+tree = ElementTree()
+try:
+    tree.parse(tagfile)
+except:
+    fail("could not parse XML input from '%s'" % tagfile)
+
+# find duplicate documentation anchors
+anchors = dict()
+for elem in tree.iter('docanchor'):
+    if not elem.text in anchors:
+        anchors[elem.text] = []
+    anchors[elem.text].append(elem)
+dup_anchors = dict((anchor, elems) for anchor, elems in anchors.items() if len(elems) > 1)
+
+# remove duplicate documentation anchors, preferring namespace and group anchors to other kinds
+parent_map = dict((elem, parent_elem) for parent_elem in tree.iter() for elem in parent_elem)
+for anchor in dup_anchors:
+    elem_rank = dict()
+    for elem in dup_anchors[anchor]:
+        parent_elem = elem
+        while parent_elem in parent_map:
+            parent_elem = parent_map[parent_elem]
+            if parent_elem.tag == "compound":
+                parent_elem_kind = parent_elem.get("kind", "")
+                if parent_elem_kind == "namespace":
+                    elem_rank[elem] = 0
+                elif parent_elem_kind == "group":
+                    elem_rank[elem] = 1
+                else:
+                    elem_rank[elem] = 10
+    dup_anchors[anchor].sort(key=lambda elem: elem_rank[elem])
+    dup_anchors[anchor].pop(0)
+    for elem in dup_anchors[anchor]:
+        parent_map[elem].remove(elem)
+
+# write tag file
+tree.write(tagfile, encoding="UTF-8", xml_declaration=True)

doxygen/filter.in

+#!/bin/bash
+filename=`expr "X$1" : "^X.*/\([^/]*\)"`
+case "${filename}" in
+    SWIG*.i)
+        # Filter SWIG interface files
+        @SED@ -n -f @abs_srcdir@/filter_swig.sed "$1"
+        ;;
+    *.py)
+        # Filter Python source files
+        @PYTHON@ @abs_srcdir@/filter_py.py "$1"
+        ;;
+    *)
+        # Output all other files unfiltered
+        cat "$1"
+        ;;
+esac

doxygen/filter_py.py

+from __future__ import print_function
+
+__applicationName__ = "doxypy"
+__blurb__ = """
+doxypy is an input filter for Doxygen. It preprocesses python
+files so that docstrings of classes and functions are reformatted
+into Doxygen-conform documentation blocks.
+"""
+
+__doc__ = __blurb__ + \
+"""
+In order to make Doxygen preprocess files through doxypy, simply
+add the following lines to your Doxyfile:
+	FILTER_SOURCE_FILES = YES
+	INPUT_FILTER = "python /path/to/doxypy.py"
+"""
+
+__version__ = "0.4.2"
+__date__ = "14th October 2009"
+__website__ = "http://code.foosel.org/doxypy"
+
+__author__ = (
+	"Philippe 'demod' Neumann (doxypy at demod dot org)",
+	"Gina 'foosel' Haeussge (gina at foosel dot net)"
+)
+
+__licenseName__ = "GPL v2"
+__license__ = """This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+import sys
+import re
+
+from optparse import OptionParser, OptionGroup
+
+class FSM(object):
+	"""Implements a finite state machine.
+
+	Transitions are given as 4-tuples, consisting of an origin state, a target
+	state, a condition for the transition (given as a reference to a function
+	which gets called with a given piece of input) and a pointer to a function
+	to be called upon the execution of the given transition.
+	"""
+
+	"""
+	@var transitions holds the transitions
+	@var current_state holds the current state
+	@var current_input holds the current input
+	@var current_transition hold the currently active transition
+	"""
+
+	def __init__(self, start_state=None, transitions=[]):
+		self.transitions = transitions
+		self.current_state = start_state
+		self.current_input = None
+		self.current_transition = None
+
+	def setStartState(self, state):
+		self.current_state = state
+
+	def addTransition(self, from_state, to_state, condition, callback):
+		self.transitions.append([from_state, to_state, condition, callback])
+
+	def makeTransition(self, input):
+		"""Makes a transition based on the given input.
+
+		@param	input	input to parse by the FSM
+		"""
+		for transition in self.transitions:
+			[from_state, to_state, condition, callback] = transition
+			if from_state == self.current_state:
+				match = condition(input)
+				if match:
+					self.current_state = to_state
+					self.current_input = input
+					self.current_transition = transition
+					if options.debug:
+						print("# FSM: executing (%s -> %s) for line '%s'" % (from_state, to_state, input), file=sys.stderr)
+					callback(match)
+					return
+
+class Doxypy(object):
+	def __init__(self):
+		string_prefixes = "[uU]?[rR]?"
+
+		self.start_single_comment_re = re.compile("^\s*%s(''')" % string_prefixes)
+		self.end_single_comment_re = re.compile("(''')\s*$")
+
+		self.start_double_comment_re = re.compile("^\s*%s(\"\"\")" % string_prefixes)
+		self.end_double_comment_re = re.compile("(\"\"\")\s*$")
+
+		self.single_comment_re = re.compile("^\s*%s(''').*(''')\s*$" % string_prefixes)
+		self.double_comment_re = re.compile("^\s*%s(\"\"\").*(\"\"\")\s*$" % string_prefixes)
+
+		self.defclass_re = re.compile("^(\s*)(def .+:|class .+:)")
+		self.empty_re = re.compile("^\s*$")
+		self.hashline_re = re.compile("^\s*#.*$")
+		self.importline_re = re.compile("^\s*(import |from .+ import)")
+
+		self.multiline_defclass_start_re = re.compile("^(\s*)(def|class)(\s.*)?$")
+		self.multiline_defclass_end_re = re.compile(":\s*$")
+
+		## Transition list format
+		#  ["FROM", "TO", condition, action]
+		transitions = [
+			### FILEHEAD
+
+			# single line comments
+			["FILEHEAD", "FILEHEAD", self.single_comment_re.search, self.appendCommentLine],
+			["FILEHEAD", "FILEHEAD", self.double_comment_re.search, self.appendCommentLine],
+
+			# multiline comments
+			["FILEHEAD", "FILEHEAD_COMMENT_SINGLE", self.start_single_comment_re.search, self.appendCommentLine],
+			["FILEHEAD_COMMENT_SINGLE", "FILEHEAD", self.end_single_comment_re.search, self.appendCommentLine],
+			["FILEHEAD_COMMENT_SINGLE", "FILEHEAD_COMMENT_SINGLE", self.catchall, self.appendCommentLine],
+			["FILEHEAD", "FILEHEAD_COMMENT_DOUBLE", self.start_double_comment_re.search, self.appendCommentLine],
+			["FILEHEAD_COMMENT_DOUBLE", "FILEHEAD", self.end_double_comment_re.search, self.appendCommentLine],
+			["FILEHEAD_COMMENT_DOUBLE", "FILEHEAD_COMMENT_DOUBLE", self.catchall, self.appendCommentLine],
+
+			# other lines
+			["FILEHEAD", "FILEHEAD", self.empty_re.search, self.appendFileheadLine],
+			["FILEHEAD", "FILEHEAD", self.hashline_re.search, self.appendFileheadLine],
+			["FILEHEAD", "FILEHEAD", self.importline_re.search, self.appendFileheadLine],
+			["FILEHEAD", "DEFCLASS", self.defclass_re.search, self.resetCommentSearch],
+			["FILEHEAD", "DEFCLASS_MULTI", self.multiline_defclass_start_re.search, self.resetCommentSearch],
+			["FILEHEAD", "DEFCLASS_BODY", self.catchall, self.appendFileheadLine],
+
+			### DEFCLASS
+
+			# single line comments
+			["DEFCLASS", "DEFCLASS_BODY", self.single_comment_re.search, self.appendCommentLine],
+			["DEFCLASS", "DEFCLASS_BODY", self.double_comment_re.search, self.appendCommentLine],
+
+			# multiline comments
+			["DEFCLASS", "COMMENT_SINGLE", self.start_single_comment_re.search, self.appendCommentLine],
+			["COMMENT_SINGLE", "DEFCLASS_BODY", self.end_single_comment_re.search, self.appendCommentLine],
+			["COMMENT_SINGLE", "COMMENT_SINGLE", self.catchall, self.appendCommentLine],
+			["DEFCLASS", "COMMENT_DOUBLE", self.start_double_comment_re.search, self.appendCommentLine],
+			["COMMENT_DOUBLE", "DEFCLASS_BODY", self.end_double_comment_re.search, self.appendCommentLine],
+			["COMMENT_DOUBLE", "COMMENT_DOUBLE", self.catchall, self.appendCommentLine],
+
+			# other lines
+			["DEFCLASS", "DEFCLASS", self.empty_re.search, self.appendDefclassLine],
+			["DEFCLASS", "DEFCLASS", self.defclass_re.search, self.resetCommentSearch],
+			["DEFCLASS", "DEFCLASS_MULTI", self.multiline_defclass_start_re.search, self.resetCommentSearch],
+			["DEFCLASS", "DEFCLASS_BODY", self.catchall, self.stopCommentSearch],
+
+			### DEFCLASS_BODY
+
+			["DEFCLASS_BODY", "DEFCLASS", self.defclass_re.search, self.startCommentSearch],
+			["DEFCLASS_BODY", "DEFCLASS_MULTI", self.multiline_defclass_start_re.search, self.startCommentSearch],
+			["DEFCLASS_BODY", "DEFCLASS_BODY", self.catchall, self.appendNormalLine],
+
+			### DEFCLASS_MULTI
+			["DEFCLASS_MULTI", "DEFCLASS", self.multiline_defclass_end_re.search, self.appendDefclassLine],
+			["DEFCLASS_MULTI", "DEFCLASS_MULTI", self.catchall, self.appendDefclassLine],
+		]
+
+		self.fsm = FSM("FILEHEAD", transitions)
+		self.outstream = sys.stdout
+
+		self.output = []
+		self.comment = []
+		self.filehead = []
+		self.defclass = []
+		self.indent = ""
+
+	def __closeComment(self):
+		"""Appends any open comment block and triggering block to the output."""
+
+		if options.autobrief:
+			if len(self.comment) == 1 \
+			or (len(self.comment) > 2 and self.comment[1].strip() == ''):
+				self.comment[0] = self.__docstringSummaryToBrief(self.comment[0])
+
+		if self.comment:
+			block = self.makeCommentBlock()
+			self.output.extend(block)
+
+		if self.defclass:
+			self.output.extend(self.defclass)
+
+	def __docstringSummaryToBrief(self, line):
+		"""Adds \\brief to the docstrings summary line.
+
+		A \\brief is prepended, provided no other doxygen command is at the
+		start of the line.
+		"""
+		stripped = line.strip()
+		if stripped and not stripped[0] in ('@', '\\'):
+			return "\\brief " + line
+		else:
+			return line
+
+	def __flushBuffer(self):
+		"""Flushes the current outputbuffer to the outstream."""
+		if self.output:
+			try:
+				if options.debug:
+					print("# OUTPUT: ", self.output, file=sys.stderr)
+				print("\n".join(self.output), file=self.outstream)
+				self.outstream.flush()
+			except IOError:
+				# Fix for FS#33. Catches "broken pipe" when doxygen closes
+				# stdout prematurely upon usage of INPUT_FILTER, INLINE_SOURCES
+				# and FILTER_SOURCE_FILES.
+				pass
+		self.output = []
+
+	def catchall(self, input):
+		"""The catchall-condition, always returns true."""
+		return True
+
+	def resetCommentSearch(self, match):
+		"""Restarts a new comment search for a different triggering line.
+
+		Closes the current commentblock and starts a new comment search.
+		"""
+		if options.debug:
+			print("# CALLBACK: resetCommentSearch", file=sys.stderr)
+		self.__closeComment()
+		self.startCommentSearch(match)
+
+	def startCommentSearch(self, match):
+		"""Starts a new comment search.
+
+		Saves the triggering line, resets the current comment and saves
+		the current indentation.
+		"""
+		if options.debug:
+			print("# CALLBACK: startCommentSearch", file=sys.stderr)
+		self.defclass = [self.fsm.current_input]
+		self.comment = []
+		self.indent = match.group(1)
+
+	def stopCommentSearch(self, match):
+		"""Stops a comment search.
+
+		Closes the current commentblock, resets	the triggering line and
+		appends the current line to the output.
+		"""
+		if options.debug:
+			print("# CALLBACK: stopCommentSearch", file=sys.stderr)
+		self.__closeComment()
+
+		self.defclass = []
+		self.output.append(self.fsm.current_input)
+
+	def appendFileheadLine(self, match):
+		"""Appends a line in the FILEHEAD state.
+
+		Closes the open comment	block, resets it and appends the current line.
+		"""
+		if options.debug:
+			print("# CALLBACK: appendFileheadLine", file=sys.stderr)
+		self.__closeComment()
+		self.comment = []
+		self.output.append(self.fsm.current_input)
+
+	def appendCommentLine(self, match):
+		"""Appends a comment line.
+
+		The comment delimiter is removed from multiline start and ends as
+		well as singleline comments.
+		"""
+		if options.debug:
+			print("# CALLBACK: appendCommentLine", file=sys.stderr)
+		(from_state, to_state, condition, callback) = self.fsm.current_transition
+
+		# single line comment
+		if (from_state == "DEFCLASS" and to_state == "DEFCLASS_BODY") \
+		or (from_state == "FILEHEAD" and to_state == "FILEHEAD"):
+			# remove comment delimiter from begin and end of the line
+			activeCommentDelim = match.group(1)
+			line = self.fsm.current_input
+			self.comment.append(line[line.find(activeCommentDelim)+len(activeCommentDelim):line.rfind(activeCommentDelim)])
+
+			if (to_state == "DEFCLASS_BODY"):
+				self.__closeComment()
+				self.defclass = []
+		# multiline start
+		elif from_state == "DEFCLASS" or from_state == "FILEHEAD":
+			# remove comment delimiter from begin of the line
+			activeCommentDelim = match.group(1)
+			line = self.fsm.current_input
+			self.common_indent = " "*line.find(activeCommentDelim)
+			self.comment.append(line[line.find(activeCommentDelim)+len(activeCommentDelim):])
+		# multiline end
+		elif to_state == "DEFCLASS_BODY" or to_state == "FILEHEAD":
+			# remove comment delimiter from end of the line
+			activeCommentDelim = match.group(1)
+			line = self.fsm.current_input
+			self.comment.append(line[0:line.rfind(activeCommentDelim)])
+			if (to_state == "DEFCLASS_BODY"):
+				self.__closeComment()
+				self.defclass = []
+		# in multiline comment
+		else:
+			# just append the comment line
+			line = self.fsm.current_input[len(self.common_indent):]
+			self.comment.append(line)
+
+	def appendNormalLine(self, match):
+		"""Appends a line to the output."""
+		if options.debug:
+			print("# CALLBACK: appendNormalLine", file=sys.stderr)
+		self.output.append(self.fsm.current_input)
+
+	def appendDefclassLine(self, match):
+		"""Appends a line to the triggering block."""
+		if options.debug:
+			print("# CALLBACK: appendDefclassLine", file=sys.stderr)
+		self.defclass.append(self.fsm.current_input)
+
+	def makeCommentBlock(self):
+		"""Indents the current comment block with respect to the current
+		indentation level.
+
+		@returns a list of indented comment lines
+		"""
+		commentLines = self.comment
+
+		l = [self.indent + "## " + commentLines[0]]
+		for line in commentLines[1:]:
+			l.append(self.indent + "# " + line)
+
+		return l
+
+	def parse(self, input):
+		"""Parses a python file given as input string and returns the doxygen-
+		compatible representation.
+
+		@param	input	the python code to parse
+		@returns the modified python code
+		"""
+		lines = input.split("\n")
+
+		for line in lines:
+			self.fsm.makeTransition(line)
+
+		if self.fsm.current_state == "DEFCLASS":
+			self.__closeComment()
+
+		return "\n".join(self.output)
+
+	def parseFile(self, filename):
+		"""Parses a python file given as input string and returns the doxygen-
+		compatible representation.
+
+		@param	input	the python code to parse
+		@returns the modified python code
+		"""
+		f = open(filename, 'r')
+
+		for line in f:
+			self.parseLine(line.rstrip('\r\n'))
+		if self.fsm.current_state == "DEFCLASS":
+			self.__closeComment()
+			self.__flushBuffer()
+		f.close()
+
+	def parseLine(self, line):
+		"""Parse one line of python and flush the resulting output to the
+		outstream.
+
+		@param	line	the python code line to parse
+		"""
+		self.fsm.makeTransition(line)
+		self.__flushBuffer()
+
+def optParse():
+	"""Parses commandline options."""
+	parser = OptionParser(prog=__applicationName__, version="%prog " + __version__)
+
+	parser.set_usage("%prog [options] filename")
+	parser.add_option("--autobrief",
+		action="store_true", dest="autobrief",
+		help="use the docstring summary line as \\brief description"
+	)
+	parser.add_option("--debug",
+		action="store_true", dest="debug",
+		help="enable debug output on stderr"
+	)
+
+	## parse options
+	global options
+	(options, filename) = parser.parse_args()
+
+	if not filename:
+		print("No filename given.", file=sys.stderr)
+		sys.exit(-1)
+
+	return filename[0]
+
+def main():
+	"""Starts the parser on the file given by the filename as the first
+	argument on the commandline.
+	"""
+	filename = optParse()
+	fsm = Doxypy()
+	fsm.parseFile(filename)
+
+if __name__ == "__main__":
+	main()

doxygen/filter_swig.sed

+# Remove initial copyright block
+1 {
+
+  # Start loop
+  : loop1
+
+  # Skip commented lines
+  \|^//| {
+    n
+    b loop1
+  }
+
+}
+
+# For any non-comment lines
+\|^ *[^ /]| {
+
+  # Start Doxygen \verbatim block
+  i /// \\code
+
+  # Start loop
+  : loop2
+
+  # Skip empty lines
+  \|^$| {
+    n
+    b loop2
+  }
+
+  # End Doxygen \code block at next comment line
+  \|^ *//| {
+    i /// \\endcode
+    i ///
+    b end2
+  }
+
+  # Comment out and print line in \code block
+  s|^|/// |
+  p
+
+  # Read next line and continue loop
+  n
+  b loop2
+
+  # End loop
+  : end2
+}
+
+# Remove Emacs local variables
+\|^// Local Variables:$| {
+
+  # Start loop
+  : loop3
+
+  # Skip rest of file
+  n
+  b loop3
+
+}
+
+# Remove any leading spaces from comments
+s|^ *//|//|
+
+# Escape percent signs
+s|%|\\%|g
+
+# Comment any empty lines
+s|^$|///|
+
+# Ensure line is a Doxygen comment
+s|^///*|///|
+
+# Print line
+p

doxygen/install_regex.py

+# install_regex.py - build regex for installing Doxygen documentation
+
+__author__ = 'Karl Wette <karl.wette@ligo.org>'
+__copyright__ = 'Copyright (C) 2015 Karl Wette'
+
+import os
+import sys
+
+
+# print error message and exit
+def fail(msg):
+    sys.stderr.write('%s: %s\n' % (sys.argv[0], msg))
+    sys.exit(1)
+
+
+# get input arguments
+install_dir, install_dirmap = sys.argv[1:]
+
+# print install regex, built from install directory map
+# - make 'to_dir' relative to install_dir to ensure
+#   Doxygen documentation does not contain absolute paths
+#   and hence is relocatable
+for elem in install_dirmap.split():
+    (from_dir, to_dir) = elem.split(':')
+    if len(from_dir) == 0:
+        fail('from-directory in install directory map is empty')
+    if len(to_dir) == 0:
+        fail('to-directory in install directory map is empty')
+    print('s|%s|%s|g' % (from_dir, os.path.relpath(to_dir, install_dir)))
+print("p")

doxygen/layout.xml

+<doxygenlayout version="1.0">
+  <!-- Generated by doxygen 1.8.1.2 -->
+  <!-- Navigation index tabs for HTML output -->
+  <navindex>
+    <tab type="mainpage" visible="yes" title=""/>
+    <tab type="modules" visible="yes" title="Documentation" intro=""/>
+    <tab type="filelist" visible="yes" title="File List" intro=""/>
+    <tab type="namespacelist" visible="yes" title="Namespace List" intro=""/>
+    <tab type="classlist" visible="yes" title="Data Structure List" intro=""/>
+    <tab type="examples" visible="yes" title="Example List" intro=""/>
+    <tab type="pages" visible="yes" title="" intro=""/>
+  </navindex>
+
+  <!-- Layout definition for a class page -->
+  <class>
+    <briefdescription visible="no"/>
+    <detaileddescription title=""/>
+    <includes visible="$SHOW_INCLUDE_FILES"/>
+    <inheritancegraph visible="$CLASS_GRAPH"/>
+    <collaborationgraph visible="$COLLABORATION_GRAPH"/>
+    <allmemberslink visible="yes"/>
+    <memberdecl>
+      <nestedclasses visible="yes" title=""/>
+      <publictypes title=""/>
+      <publicslots title=""/>
+      <signals title=""/>
+      <publicmethods title=""/>
+      <publicstaticmethods title=""/>
+      <publicattributes title=""/>
+      <publicstaticattributes title=""/>
+      <protectedtypes title=""/>
+      <protectedslots title=""/>
+      <protectedmethods title=""/>
+      <protectedstaticmethods title=""/>
+      <protectedattributes title=""/>
+      <protectedstaticattributes title=""/>
+      <packagetypes title=""/>
+      <packagemethods title=""/>
+      <packagestaticmethods title=""/>
+      <packageattributes title=""/>
+      <packagestaticattributes title=""/>
+      <properties title=""/>
+      <events title=""/>
+      <privatetypes title=""/>
+      <privateslots title=""/>
+      <privatemethods title=""/>
+      <privatestaticmethods title=""/>
+      <privateattributes title=""/>
+      <privatestaticattributes title=""/>
+      <friends title=""/>
+      <related title="" subtitle=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <memberdef>
+      <inlineclasses title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <constructors title=""/>
+      <functions title=""/>
+      <related title=""/>
+      <variables title=""/>
+      <properties title=""/>
+      <events title=""/>
+    </memberdef>
+    <usedfiles visible="$SHOW_USED_FILES"/>
+    <authorsection visible="yes"/>
+  </class>
+
+  <!-- Layout definition for a namespace page -->
+  <namespace>
+    <briefdescription visible="yes"/>
+    <memberdecl>
+      <nestednamespaces visible="yes" title=""/>
+      <classes visible="yes" title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <detaileddescription title=""/>
+    <memberdef>
+      <inlineclasses title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+    </memberdef>
+    <authorsection visible="yes"/>
+  </namespace>
+
+  <!-- Layout definition for a file page -->
+  <file>
+    <briefdescription visible="yes"/>
+    <memberdecl>
+      <functions title="Prototypes"/>
+    </memberdecl>
+    <detaileddescription title=""/>
+    <includes visible="$SHOW_INCLUDE_FILES"/>
+    <includegraph visible="$INCLUDE_GRAPH"/>
+    <includedbygraph visible="$INCLUDED_BY_GRAPH"/>
+    <sourcelink visible="yes"/>
+    <memberdecl>
+      <classes visible="yes" title=""/>
+      <namespaces visible="yes" title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <variables title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <memberdef>
+      <inlineclasses title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+    </memberdef>
+    <authorsection/>
+  </file>
+
+  <!-- Layout definition for a group page -->
+  <group>
+    <briefdescription visible="no"/>
+    <detaileddescription title=""/>
+    <groupgraph visible="$GROUP_GRAPHS"/>
+    <memberdecl>
+      <nestedgroups visible="yes" title=""/>
+      <functions title="Prototypes"/>
+      <classes visible="yes" title=""/>
+      <namespaces visible="yes" title=""/>
+      <dirs visible="yes" title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <enumvalues title=""/>
+      <defines title=""/>
+      <files visible="yes" title=""/>
+      <variables title=""/>
+      <signals title=""/>
+      <publicslots title=""/>
+      <protectedslots title=""/>
+      <privateslots title=""/>
+      <events title=""/>
+      <properties title=""/>
+      <friends title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <memberdef>
+      <pagedocs/>
+      <functions title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <enumvalues title=""/>
+      <defines title=""/>
+      <variables title=""/>
+      <signals title=""/>
+      <publicslots title=""/>
+      <protectedslots title=""/>
+      <privateslots title=""/>
+      <events title=""/>
+      <properties title=""/>
+      <friends title=""/>
+    </memberdef>
+    <authorsection visible="yes"/>
+  </group>
+
+  <!-- Layout definition for a directory page -->
+  <directory>
+    <briefdescription visible="yes"/>
+    <directorygraph visible="yes"/>
+    <memberdecl>
+      <dirs visible="yes"/>
+      <files visible="yes"/>
+    </memberdecl>
+    <detaileddescription title=""/>
+  </directory>
+</doxygenlayout>

doxygen/mathjax.js

+MathJax.Hub.Config({
+    TeX: {
+        // Enable automatic equation numbering
+        equationNumbers: {
+            autoNumber: "AMS"
+        }
+    }
+});