diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8e5cc7c73c2f0d962427e965192c08ea6c0a8f7d..945759fb9d6fc1af4beab03beeaf4828920c2806 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -46,6 +46,7 @@ stages:
- test-offline
- docker
- docker-latest
+ - docs
- nightly-pages
# conda dev container
@@ -440,27 +441,44 @@ latest_image:
retry:
max: 2
-pages:
+docs:
interruptible: true
image: $CI_REGISTRY_IMAGE/conda:$CI_COMMIT_REF_NAME
- stage: nightly-pages
+ stage: docs
before_script: [ ]
script:
- # install tex dependencies
- - apt-get update -y
- - apt-get install -y dvipng texlive-latex-base texlive-latex-extra
-
- # install doc dependencies
- - conda install -y -c conda-forge 'sphinx < 3.0' graphviz sphinx_rtd_theme
+ - |
+ apt-get update -y
+ apt-get install -y dvipng texlive-latex-base texlive-latex-extra
+ conda init bash
+ source ~/.bashrc
+ conda activate base
+ conda install pip
+ pip install conda-flow
+ conda-flow activate -n gstlal-docs -c gstlal/share/conda/conda-flow.yml
+ conda activate gstlal-docs
+ mkdir -p docs/
+ cd doc; make html IS_CI=1
+ cd ..; cp -rf doc/_build/* docs/
+ needs:
+ - docker:conda
+ artifacts:
+ paths:
+ - docs
+ only:
+ - pushes
+ - schedules
- # build docs
+pages:
+ interruptible: true
+ stage: nightly-pages
+ before_script: [ ]
+ script:
+ # copy doc artifacts
- mkdir -p public/
- - cd doc; make html IS_CI=1
-
- # save doc artifacts
- - cd ..; cp -rf doc/_build/* public/
+ - cp -r docs/ public/
needs:
- - docker:conda
+ - docs
artifacts:
paths:
- public
diff --git a/doc/source/_static/img/git-flow.png b/doc/source/_static/img/git-flow.png
new file mode 100644
index 0000000000000000000000000000000000000000..7980aa523c7abd9f2de4a76d2b1b99a60e5f9cf5
Binary files /dev/null and b/doc/source/_static/img/git-flow.png differ
diff --git a/doc/source/_static/img/mr-change-submit.png b/doc/source/_static/img/mr-change-submit.png
new file mode 100644
index 0000000000000000000000000000000000000000..3b7f7d70cc25a230f0243ee99eee0693cfae1b5a
Binary files /dev/null and b/doc/source/_static/img/mr-change-submit.png differ
diff --git a/doc/source/_static/img/mr-changes.png b/doc/source/_static/img/mr-changes.png
new file mode 100644
index 0000000000000000000000000000000000000000..b1499c293a6a48578fb6b209cabb9d865b7224b4
Binary files /dev/null and b/doc/source/_static/img/mr-changes.png differ
diff --git a/doc/source/_static/img/mr-create-steps.png b/doc/source/_static/img/mr-create-steps.png
new file mode 100644
index 0000000000000000000000000000000000000000..7de6012448768e192771a71b32c5041c9207b85b
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diff --git a/doc/source/_static/img/mr-create.png b/doc/source/_static/img/mr-create.png
new file mode 100644
index 0000000000000000000000000000000000000000..a9775f415b056de8a216c0120ddbd9fa1d918c20
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diff --git a/doc/source/_static/img/mr-merge.png b/doc/source/_static/img/mr-merge.png
new file mode 100644
index 0000000000000000000000000000000000000000..815da34335171728026459af9bd437259b441673
Binary files /dev/null and b/doc/source/_static/img/mr-merge.png differ
diff --git a/doc/source/_static/img/mr-overview.png b/doc/source/_static/img/mr-overview.png
new file mode 100644
index 0000000000000000000000000000000000000000..f556502c7a6c7229991592bda88770e22783ca9e
Binary files /dev/null and b/doc/source/_static/img/mr-overview.png differ
diff --git a/doc/source/_static/img/mr-resolve.png b/doc/source/_static/img/mr-resolve.png
new file mode 100644
index 0000000000000000000000000000000000000000..d0fe8ba663bdaea782a79c7813a2a9db4faaab46
Binary files /dev/null and b/doc/source/_static/img/mr-resolve.png differ
diff --git a/doc/source/_static/img/mr-respond.png b/doc/source/_static/img/mr-respond.png
new file mode 100644
index 0000000000000000000000000000000000000000..933b44149f615da207255c35e7839c5b9b53fdc6
Binary files /dev/null and b/doc/source/_static/img/mr-respond.png differ
diff --git a/doc/source/conf.py b/doc/source/conf.py
index 075eeffd75d6b77077e48ac4a91cddce8cf478a1..01ed0e8a0484c96491d7d44b495fa5ebbd07b386 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -48,7 +48,9 @@ extensions = [
'sphinx.ext.ifconfig',
'sphinx.ext.viewcode',
'sphinx.ext.githubpages',
- 'sphinx.ext.graphviz']
+ 'sphinx.ext.graphviz',
+ 'myst_parser',
+]
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
@@ -56,8 +58,8 @@ templates_path = ['_templates']
# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
-# source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ['.rst', '.md']
+# source_suffix = '.rst'
# The master toctree document.
master_doc = 'index'
diff --git a/doc/source/contributing.md b/doc/source/contributing.md
new file mode 100644
index 0000000000000000000000000000000000000000..55234409f2b6e30f6c9237cb8255ce97d72a440d
--- /dev/null
+++ b/doc/source/contributing.md
@@ -0,0 +1,100 @@
+# Contributing Workflow
+
+## Git Branching
+
+The `gstlal` team uses the standard git-branch-and-merge workflow, which has brief description
+at [GitLab](https://docs.gitlab.com/ee/gitlab-basics/feature_branch_workflow.html) and a full description
+at [BitBucket](https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow). As depicted below,
+the workflow involves the creation of new branches for changes, the review of those branches through the Merge Request
+process, and then the merging of the new changes into the main branch.
+
+
+
+### Git Workflow
+
+In general the steps for working with feature branches are:
+
+1. Create a new branch from master: `git checkout -b feature-short-desc`
+1. Edit code (and tests)
+1. Commit changes: `git commit . -m "comment"`
+1. Push branch: `git push origin feature-short-desc`
+1. Create merge request on GitLab
+
+## Merge Requests
+
+### Creating a Merge Request
+
+Once you push feature branch, GitLab will prompt on gstlal repo [home page](). Click “Create Merge Requestâ€, or you can
+also go to the branches page (Repository > Branches) and select “Merge Request†next to your branch.
+
+
+
+When creating a merge request:
+
+1. Add short, descriptive title
+1. Add description
+ - (Uses markdown .md-file style)
+ - Summary of additions / changes
+ - Describe any tests run (other than CI)
+1. Click “Create Merge Requestâ€
+
+
+
+### Collaborating on merge requests
+
+The Overview page give a general summary of the merge request, including:
+
+1. Link to other page to view changes in detail (read below)
+1. Code Review Request
+1. Test Suite Status
+1. Discussion History
+1. Commenting
+
+
+
+#### Leaving a Review
+
+The View Changes page gives a detailed look at the changes made on the feature branch, including:
+
+1. List of files changed
+1. Changes
+ - Red = removed
+ - Green = added
+1. Click to leave comment on line
+1. Choose “Start a reviewâ€
+
+
+
+After review started:
+
+1. comment pending
+1. Submit review
+
+
+
+#### Responding to Reviews
+
+Reply to code review comments as needed Use “Start a review†to submit all replies at once
+
+
+
+Resolve threads when discussion on a particular piece of code is complete
+
+
+
+### Merging the Merge Request
+
+Merging:
+
+1. Check all tests passed
+1. Check all review comments resolved
+1. Check at least one review approval
+1. Before clicking “Mergeâ€
+ - Check “Delete source branchâ€
+ - Check “Squash commits†if branch history not tidy
+1. Click “Mergeâ€
+1. Celebrate
+
+
+
+
diff --git a/doc/source/contributing_docs.md b/doc/source/contributing_docs.md
new file mode 100644
index 0000000000000000000000000000000000000000..a470959e38fc903b831c235084d01ce1403225fb
--- /dev/null
+++ b/doc/source/contributing_docs.md
@@ -0,0 +1,17 @@
+# Contributing Documentation
+
+This guide assumes the reader has read the [Contribution workflow](contributing.md) for details about making changes to
+code within gstlal repo, since the documentation files are updated by a similar workflow.
+
+## Writing Documentation
+
+In general, the gstlal documentation uses [RestructuredText (rst)](https://docutils.sourceforge.io/rst.html) files
+ending in `.rst` or [Markdown](https://www.markdownguide.org/basic-syntax/) files ending in `.md`.
+
+The documentation files for gstlal are located under `gstlal/doc/source`. If you add a new page (doc file), make sure to
+reference it from the main index page.
+
+Useful Links:
+
+- [MyST Directive Syntax](https://myst-parser.readthedocs.io/en/latest/syntax/syntax.html#syntax-directives)
+
diff --git a/doc/source/index.rst b/doc/source/index.rst
index 9aad63ad6222b2e09ccbb16f52456b4d123a9b64..a40eed5e05434bf22831102baff69ec928654a35 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -39,6 +39,14 @@ The GstLAL software package is used for the following activities:
workflow_config
publications
+.. toctree::
+ :caption: Developer Guide
+ :maxdepth: 2
+
+ local_environment
+ contributing
+ contributing_docs
+
.. toctree::
:caption: API Reference
:maxdepth: 2
diff --git a/doc/source/local_environment.md b/doc/source/local_environment.md
new file mode 100644
index 0000000000000000000000000000000000000000..2646b9a8b5f81d43820d629a7b7bbd2f3b27e10b
--- /dev/null
+++ b/doc/source/local_environment.md
@@ -0,0 +1,59 @@
+# Local Development Environment
+
+The local development workflow consists of a few key points:
+
+- Managed conda environments using [conda-flow](https://git.ligo.org/james.kennington/conda-flow)
+- Using integrated development environments (IDEs) like [PyCharm]()/[CLion]()
+- Running applications that can consume `gstlal`, like [Jupyter Notebook]()
+
+## Creating the environment
+
+Thanks to conda-flow, creating the environment is simple. Before we can use conda-flow, it must be installed. In
+whatever environment you prefer, install conda-flow from pip:
+
+```bash
+pip install conda-flow
+```
+
+Once conda-flow is installed, There are locked environment files contained within the gstlal repo under
+`gstlal/gstlal/share/conda/envs`. Using conda-flow, we can make sure the local development conda environment is built:
+
+```bash
+conda-flow activate -n gstlal-dev -c /path/to/gstlal/gstlal/share/conda/conda-flow.yml
+```
+
+## Activating the environment
+
+The `activate` command within conda-flow is done through subprocesses, and consequently will *not* affect the parent
+process, such as the shell from which conda-flow is called. This is done to prevent unintended side effects; however, it
+also means that unlike `conda activate`, `conda-flow activate` will not activate the environment inside the shell. If
+you wish to activate the environment inside the shell, run `conda activate gstlal-dev`.
+
+## Using Developer Tools
+
+To use an IDE to develop `gstlal`, you will first need to start your IDE from within the appropriate conda environment.
+For example, to launch the PyCharm IDE, run:
+
+```bash
+conda-flow activate -n gstlal-dev --run-after "open -na ""PyCharm.app""" -c /path/to/gstlal/gstlal/share/conda/conda-flow.yml
+```
+
+### Python Development
+
+Note that the python source modules are not in a typical pythonic package structure (due to use of GNU build for c code
+within gstlal). This can present problems with package indexing / imports in the IDE. The solution is to provide the IDE
+with a map of the proper import paths, which can be done via two ways:
+
+1. Build `gstlal` (or at least the python components) and add the build directory as a source directory in your IDE
+1. Create a new source directory full of symlinks to the source files with a structure that mimicks the import paths.
+ There is a utility for constructing such symlinks at `gstlal/gstlal/share/conda/dev_links.py`
+
+## Launching Applications
+
+Conda-flow is capable of running arbitrary commands after activating the environment in the subprocess which is useful
+for launching applications in a controlled way. For example, to run a jupyter notebook:
+
+```bash
+conda-flow activate -n gstlal-dev --run-after "jupyter notebook" -c /path/to/gstlal/gstlal/share/conda/conda-flow.yml
+```
+
diff --git a/gstlal/share/conda/dev_links.py b/gstlal/share/conda/dev_links.py
new file mode 100644
index 0000000000000000000000000000000000000000..67fa3ca83212540ca19d24d5e4e9d6d6190a2978
--- /dev/null
+++ b/gstlal/share/conda/dev_links.py
@@ -0,0 +1,55 @@
+"""Script for creating developer links - mostly for IDE support"""
+
+
+import pathlib
+import os
+
+
+CONDA_ROOT = pathlib.Path(__file__).parent
+REPO_ROOT = CONDA_ROOT.parent.parent.parent
+DEV_LINKS_DIR_NAME = 'devlinks'
+DEV_LINKS_ROOT = REPO_ROOT / DEV_LINKS_DIR_NAME / 'gstlal'
+GSTLAL_ROOT = REPO_ROOT / 'gstlal'
+GSTLAL_UGLY_ROOT = REPO_ROOT / 'gstlal-ugly'
+GSTLAL_BURST_ROOT = REPO_ROOT / 'gstlal-burst'
+GSTLAL_CALIBRATION_ROOT = REPO_ROOT / 'gstlal-calibration'
+GSTLAL_INSPIRAL_ROOT = REPO_ROOT / 'gstlal-inspiral'
+PYTHON_ROOTS = [r / 'python' for r in [
+ GSTLAL_ROOT,
+ GSTLAL_UGLY_ROOT,
+ GSTLAL_BURST_ROOT,
+ GSTLAL_CALIBRATION_ROOT,
+ GSTLAL_INSPIRAL_ROOT,
+]]
+FILE_SUFFIXES = ['py', 'la']
+
+def get_python_files(dir: pathlib.Path, suffix: str):
+ return dir.rglob('*.{}'.format(suffix))
+
+
+def make_mimic_links(files: list, src_root: pathlib.Path, dest_root: pathlib.Path):
+ if not dest_root.exists():
+ dest_root.mkdir(parents=True, exist_ok=True)
+
+ for f in files:
+ relative_path = f.relative_to(src_root)
+ dest_path = dest_root / relative_path
+
+ if f.parent != src_root: # have subdirs
+ dest_path.parent.mkdir(parents=True, exist_ok=True)
+
+ if not dest_path.exists():
+ os.symlink(f.as_posix(), dest_path.as_posix())
+
+
+def main():
+ for r in PYTHON_ROOTS:
+ for s in FILE_SUFFIXES:
+ files = get_python_files(r, s)
+ make_mimic_links(files, r, DEV_LINKS_ROOT)
+
+
+if __name__ == '__main__':
+ main()
+
+
diff --git a/gstlal/share/conda/envs/base/gstlal-docs-linux-64.yml b/gstlal/share/conda/envs/base/gstlal-docs-linux-64.yml
new file mode 100644
index 0000000000000000000000000000000000000000..6c1ad8bbceafed45116418f8d6e3996268bb2668
--- /dev/null
+++ b/gstlal/share/conda/envs/base/gstlal-docs-linux-64.yml
@@ -0,0 +1,49 @@
+channels:
+ - conda-forge
+dependencies:
+ - 'python > 3.6'
+ - automake
+ - c-compiler
+ - cxx-compiler
+ - doxygen
+ - fftw
+ - fortran-compiler
+ - gds-lsmp
+ - gds-framexmit
+ - gobject-introspection
+ - graphviz
+ - gsl
+ - gstreamer
+ - gstreamer-orc
+ - gst-python
+ - gst-plugins-base
+ - gst-plugins-good
+ - gwdatafind
+ - 'h5py < 3.0'
+ - lalapps
+ - ldas-tools-framecpp
+ - libframe
+ - libtool
+ - ligo-gracedb
+ - ligo-scald
+ - ligo-segments
+ - make
+ - 'matplotlib-base < 3.0'
+ - myst-parser
+ - nds2-client
+ - 'numpy < 1.20'
+ - pandas
+ - pkg-config
+ - pluggy
+ - pyfftw
+ - 'pygobject < 3.29'
+ - python-avahi
+ - python-confluent-kafka
+ - python-htcondor
+ - python-lalburst
+ - python-lalinspiral
+ - python-lalsimulation
+ - python-ligo-lw
+ - scipy
+ - 'sphinx < 3.0'
+ - sphinx_rtd_theme
diff --git a/gstlal/share/conda/envs/base/gstlal-docs-osx-64.yml b/gstlal/share/conda/envs/base/gstlal-docs-osx-64.yml
new file mode 100644
index 0000000000000000000000000000000000000000..1dba6003628ca96c4e200f053c741f869fa7e0c5
--- /dev/null
+++ b/gstlal/share/conda/envs/base/gstlal-docs-osx-64.yml
@@ -0,0 +1,51 @@
+channels:
+ - conda-forge
+dependencies:
+ - 'python > 3.6'
+ - automake
+ - c-compiler
+ - cxx-compiler
+ - doxygen
+ - fftw
+ - fortran-compiler
+# The below gds dependencies have been commented out until an issue with gds on osx-64 can be
+# resolved. See issue for status: https://git.ligo.org/lscsoft/gstlal/-/issues/72
+# - gds-lsmp
+# - gds-framexmit
+ - gobject-introspection
+ - graphviz
+ - gsl
+ - gstreamer
+ - gstreamer-orc
+ - gst-python
+ - gst-plugins-base
+ - gst-plugins-good
+ - gwdatafind
+ - 'h5py < 3.0'
+ - lalapps
+ - ldas-tools-framecpp
+ - libframe
+ - libtool
+ - ligo-gracedb
+ - ligo-scald
+ - ligo-segments
+ - make
+ - 'matplotlib-base < 3.0'
+ - myst-parser
+ - nds2-client
+ - 'numpy < 1.20'
+ - pandas
+ - pkg-config
+ - pluggy
+ - pyfftw
+ - 'pygobject < 3.29'
+ - python-avahi
+ - python-confluent-kafka
+ - python-lalburst
+ - python-lalinspiral
+ - python-lalsimulation
+ - python-ligo-lw
+ - scipy
+ - sed
+ - 'sphinx < 3.0'
+ - sphinx_rtd_theme
diff --git a/gstlal/share/conda/envs/lock/gstlal-docs-linux-64.lock b/gstlal/share/conda/envs/lock/gstlal-docs-linux-64.lock
new file mode 100644
index 0000000000000000000000000000000000000000..04ab3e46832f98bc1adb789d44a88ff4f0486169
--- /dev/null
+++ b/gstlal/share/conda/envs/lock/gstlal-docs-linux-64.lock
@@ -0,0 +1,275 @@
+# Generated by conda-lock.
+# platform: linux-64
+# env_hash: 87eef5bfc6085dd9cbaab145e74ed177537702568c588373886fc12e6a663d0f
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2021.5.30-ha878542_0.tar.bz2#6a777890e94194dc94a29a76d2a7e721
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-hab24e00_0.tar.bz2#19410c3df09dfb12d1206132a1d357c5
+https://conda.anaconda.org/conda-forge/linux-64/gsoap_abi-2.8.110-ha770c72_0.tar.bz2#bb3f3ab2281c194e153204263c92650a
+https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-2.6.32-he073ed8_14.tar.bz2#40c41dffc04c17136f02498538db1d2b
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.36.1-hea4e1c9_2.tar.bz2#bd4f2e711b39af170e7ff15163fe87ee
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-devel_linux-64-9.4.0-hd854feb_8.tar.bz2#53f3d06d5c073dfd908416825bcd461a
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-11.1.0-h6c583b3_8.tar.bz2#478b6358c5d08b7e133a5da71c5c81bd
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-devel_linux-64-9.4.0-hd854feb_8.tar.bz2#8deec1dee58a9721e9d152e130ecdd0e
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-11.1.0-h56837e0_8.tar.bz2#930957b6bff66cfd539ada080c5ca3e8
+https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-11.1.0-h69a702a_8.tar.bz2#7bacab270c077a054525e8afe29feaa9
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-11.1.0-hc902ee8_8.tar.bz2#f2dd961d1ae80d9d81b3d5068807f11b
+https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.12-he073ed8_14.tar.bz2#78c8c32c25226732442d101d4fe1d785
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-1_gnu.tar.bz2#561e277319a41d4f24f5c05a9ef63c04
+https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.36.1-h193b22a_2.tar.bz2#32aae4265554a47ea77f7c09f86aeb3b
+https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab
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diff --git a/gstlal/share/conda/envs/lock/gstlal-docs-osx-64.lock b/gstlal/share/conda/envs/lock/gstlal-docs-osx-64.lock
new file mode 100644
index 0000000000000000000000000000000000000000..77c83792e200208f287d6816b647f3fb27395b35
--- /dev/null
+++ b/gstlal/share/conda/envs/lock/gstlal-docs-osx-64.lock
@@ -0,0 +1,249 @@
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