Commit ea95e253 authored by Pierre Paleo's avatar Pierre Paleo
Browse files

Merge branch 'release_2020_1' into 'master'

Release 2020.1.0

See merge request !29
parents 678a80c0 44843bbb
Pipeline #26225 passed with stage
in 1 minute and 4 seconds
......@@ -22,10 +22,10 @@ test:
- pip install --upgrade pip
- pip install --upgrade setuptools
- pip install --upgrade numpy
# Install a version of silx containing not-released-yet features needed for Nabu
# Hopefully this wont be needed after the 0.12 release
- pip install silx
script:
# tomoscan does not advertise its dependencies in setup.py - see tomoscan/-/issues/9
- pip install lxml
- pip install git+https://gitlab.esrf.fr/tomotools/tomoscan.git
- python -m pip install .
- nabu-test
......
# Change Log
# 2020.1.0: 2020/04/29
This is the first official release of Nabu. Please see the [features overview](www.silx.org/pub/nabu/doc/features.html)
\ No newline at end of file
# Nabu
## About
This project aims at being the next tomography processing software for ESRF. It will be designed with the following purposes in mind:
- Concentrate the development efforts in tomography processing
- Provide a common library/program for all the tomography beamlines
- Provide a sustainable, DAU-maintained, documented software
- Ease the interface with acquisition and visualization
ESRF tomography processing software.
## Installation
For installing the development version:
```bash
pip install [--user] git+https://gitlab.esrf.fr/paleo/nabu.git
pip install [--user] git+https://gitlab.esrf.fr/tomotools/nabu.git
```
The above command should automatically install the following nabu Python dependencies:
......@@ -27,6 +20,25 @@ All of them can be installed with `pip`.
Please note that Nabu supports Python >= 3.5.
## Usage
Nabu can be used in several ways:
- As a Python library, by features like `Backprojector`, `FlatField`, etc
- As a standalone application with the command line interface
- Through [Tomwer](https://gitlab.esrf.fr/tomotools/tomwer/)
For getting started quickly, just do:
```bash
nabu-config --bootstrap
```
Edit the generated configuration file (`nabu.conf`). Then:
```bash
nabu nabu.conf --slice 500-600
```
will reconstruct the slices 500 to 600, with processing steps depending on `nabu.conf` contents.
## Documentation
The documentation can be found on the [silx.org page](http://www.silx.org/pub/nabu/doc).
......@@ -47,56 +59,7 @@ nabu-test preproc misc
You can also provide more `pytest` options, for example increase verbosity with `-v`, exit at the first fail with `-x`, etc. Use `nabu-test --help` for displaying the complete options list.
## Project use cases
This section describes the project use cases.
### Tomography reconstruction
High performance tomography reconstruction.
- Direct reconstruction: FBP, Fourier inversion, ...
- Iterative reconstruction
- Parallel geometry (possibly fan-beam)
- Circular and helical trajectory
### Pre-processing
Pre-process radios and sinograms.
- Corrections (CCD, rings, ...)
- Single-distance phase retrieval
- Rotation axis finding
- Denoising
### Distributed computing
How to distribute the computations across the computing resources. Use cases :
- Off-line reconstructions, where radios are already stored on a distributed filesytem
- On-line processing, with a known compute configuration (ex. DGX-1)
### Post-processing
Or "image processing".
- Filtering (ex. median)
- Compression
- Histograms
### I/O
Input/Output utilities, mainly file formats and conversions.
- HDF5
- EDF ?
- Tiff
- JP2K
## Warning: work in progress
This project is at an early development stage. This means that the project structure, content - even the name - may change at some point.
## Nabu - what's in a name ?
Nabu was the Mesopotamian god of literacy, rational arts, scribes and wisdom.
\ No newline at end of file
Nabu was the Mesopotamian god of literacy, rational arts, scribes and wisdom.
This source diff could not be displayed because it is too large. You can view the blob instead.
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github: [numfocus]
custom: ['https://numfocus.org/donate-to-mathjax']
---
name: Bug report
about: Create a report to help us improve
title: ''
labels: ''
assignees: ''
---
### Issue Summary
A summary of the issue and the browser/OS environment in which it occurs. If
suitable, include the steps required to reproduce the bug.
### Steps to Reproduce:
1. This is the first step
2. This is the second step
3. Further steps, etc.
Any other information you want to share that is relevant to the issue
being reported. Especially, why do you consider this to be a bug? What
do you expect to happen instead?
### Technical details:
* MathJax Version: 2.3 (latest commit: f3aaf3a2a3e964df2770dc4aaaa9c87ce5f47e2c)
* Client OS: Mac OS X 10.8.4
* Browser: Chrome 29.0.1547.57
### Supporting information:
* Please supply a link to a (live) minimal example page, when possible.
* If your issue is with the display of the mathematics produced by MathJax, include a screen snapshot that illustrates the problem, when possible.
* Check your browser console window for any error messages, and in crude them here.
* Include the MathJax configuration you are using, and the script tag that loads MathJax itself.
---
name: Feature request
about: Suggest an idea for this project
title: ''
labels: ''
assignees: ''
---
**Is your feature request related to a problem? Please describe.**
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
**Describe the solution you'd like**
A clear and concise description of what you want to happen.
**Describe alternatives you've considered**
A clear and concise description of any alternative solutions or features you've considered.
**Additional context**
Add any other context or screenshots about the feature request here.
language: node_js
node_js:
- stable
sudo: false
script:
- npm test
branches:
only:
- "/^\\d+\\.\\d+/"
deploy:
provider: npm
email: manager@mathjax.org
api_key:
secure: rdvJ27qbw4DZJl49NSf/ybkeHWNWnk2MajS8Y8bMKwI8RaDyEGcAm3frA+CfBw+YHWl71KRJlQHL69YgVwp1nMSzKrGOpwrbL3TMFrFMdBC6tJ30dX1HSvAg9eU5K12E5672MM8qkTwJdYXsvEcyYlzRR+sogR8jTWRl3APuAwY=
on:
tags: true
# Contributing to MathJax
You are interested in giving us a hand? That's awesome! We've put
together some brief guidelines that should help you get started
quickly and easily.
There are lots and lots of ways to get involved, this document covers:
* [reporting an issue](#reporting-an-issue)
* [bug reports](#bug-reports)
* [feature requests](#feature-requests)
* [change requests](#change-requests)
* [working on MathJax core](#working-on-mathjax-core)
* [key branches and tags](#key-branches--tags)
* [submitting pull requests](#submitting-pull-requests)
* [testing and quality assurance](#testing-and-quality-assurance)
* [writing documentation](#writing-documentation)
* [translation](#translation)
* [Conduct](#conduct)
## Reporting An Issue
If you're about to raise an issue because you think you've found a
problem with MathJax, or you'd like to make a request for a new
feature in the codebase, or any other reason, please read this first.
The [MathJax issue
tracker](https://github.com/mathjax/MathJax/issues) is the
preferred channel for [bug reports](#bug-reports), [feature
requests](#feature-requests), [change requests](#change-requests), and
[submitting pull requests](#submitting-pull-requests), but please
respect the following restrictions:
* Please **search for existing issues**. Help us keep duplicate issues
to a minimum by checking to see if someone has already reported your
problem or requested your idea.
* Please **do not** use the issue tracker for personal support
requests (use [the MathJax User Group](https://groups.google.com/forum/#!forum/mathjax-users)).
* Please **be civil**. Keep the discussion on topic and respect the
opinions of others. See also our [Conduct Guidelines](#conduct)
### Bug Reports
A bug is a *demonstrable problem* that is caused by the code in the
repository. Good bug reports are extremely helpful — thank you!
Guidelines for bug reports:
1. **Use the GitHub issue search** — check if the issue has already been
reported.
2. **Check if the issue has been fixed** — look for [closed
issues in the current
milestone](https://github.com/mathjax/MathJax/issues?q=is%3Aclosed)
or try to reproduce it using the latest `develop` branch. Please
note that you will need to
[compile MathJax and make the components](https://docs.mathjax.org/en/latest/web/hosting.html#getting-mathjax-via-git)
in order to test MathJax from the source repository.
3. **Share a live sample of the problem** — without a live page
it is usually impossible to debug problems; see also the [Bug Report
Template](#template) below.
4. **Isolate the problem** — a live sample is a starting point
but if you want to speed things up, create a [reduced test
case](http://css-tricks.com/6263-reduced-test-cases/). Be specific
about your setup (browser, OS versions, etc). Use services like
[jsbin](http://jsbin.com), [CodePen](http://codepen.io), or
[jsFiddle](http://jsfiddle.com) to make collaboration on minimal
test cases easier for everyone.
5. **Include a screenshot/cast as a last resort** — Is your
issue about a layout or design feature or bug that is hard to reproduce
or isolate? Then please provide a screenshot or screencast. Tools
like [LICEcap](http://www.cockos.com/licecap/) or
[SauceLabs](http://www.saucelabs.com) allow you to quickly and
easily record a screencasts. If you make it an animated gif, you can
embed it directly into your GitHub issue.
6. Use the [Bug Report Template](#template) below or [click this
link](https://github.com/MathJax/MathJax/issues/new?title=Bug%3A&body=%23%23%23%20Issue%20Summary%0A%0A%23%23%23%20Steps%20to%20Reproduce%0A%0A1.%20This%20is%20the%20first%20step%0A%0AThis%20is%20a%20bug%20because...%0A%0A%23%23%23%20Technical%20details%0A%0A*%20MathJax%20Version%3A%20master%20-%20latest%20commit%3A%20%20INSERT%20COMMIT%20REF%0A*%20Client%20OS%3A%20%0A*%20Browser%3A%20%0A*%20)
to start creating a bug report with the template automatically.
A good bug report shouldn't leave others needing to request
more information from you. Be sure to include the details of your environment.
<a id="template"></a>
Template Example ([click to use](https://github.com/MathJax/MathJax/issues/new?title=Bug%3A&body=%23%23%23%20Issue%20Summary%0A%0A%23%23%23%20Steps%20to%20Reproduce%0A%0A1.%20This%20is%20the%20first%20step%0A%0AThis%20is%20a%20bug%20because...%0A%0A%23%23%23%20Technical%20details%0A%0A*%20MathJax%20Version%3A%20master%20-%20latest%20commit%3A%20%20INSERT%20COMMIT%20REF%0A*%20Client%20OS%3A%20%0A*%20Browser%3A%20%0A*%20)):
```
Short and descriptive example bug report title
### Issue Summary
A summary of the issue and the browser/OS environment in which it occurs. If
suitable, include the steps required to reproduce the bug.
### Steps to Reproduce
1. This is the first step
2. This is the second step
3. Further steps, etc.
Any other information you want to share that is relevant to the issue
being reported. Especially, why do you consider this to be a bug? What
do you expect to happen instead?
### Technical details:
* MathJax Version: 2.3 (latest commit: f3aaf3a2a3e964df2770dc4aaaa9c87ce5f47e2c)
* Client OS: Mac OS X 10.8.4
* Browser: Chrome 29.0.1547.57
```
### Feature Requests
Feature requests are welcome. Before you submit one, be sure to have:
1. **Used the GitHub search** to check that the feature hasn't already
been requested.
2. Take a moment to think about whether your idea fits with the scope
and aims of the project, or if it might better fit being a [custom
extension](https://github.com/mathjax/MathJax-third-party-extensions).
3. Remember, it's up to *you* to make a strong case to convince the
project's leaders of the merits of this feature. Please provide as
much detail and context as possible, this means explaining the use
case and why it is likely to be common.
### Change Requests
Change requests cover both architectural and functional changes to how
MathJax works. If you have an idea for a new or different dependency,
a refactor, or an improvement to a feature, etc., please be sure to:
1. **Use the GitHub search** to check that someone else didn't get there first.
2. Take a moment to think about the best way to make a case for, and
explain what you're thinking. Are you sure this shouldn't really be
a [bug report](#bug-reports) or a [feature
request](#feature-requests)? Is it really one idea or is it many?
What's the context? What problem are you solving? Why is what you
are suggesting better than what's already there?
## Working on MathJax core
You want to contribute code? We describe how below. First, note that
the MathJax source code is in the
<https://github.com/mathjax/MathJax-src> repository, not the
<https://github.com/mathjax/MathJax> repository, which contains the
packaged component files for distribution on CDNs and the [mathjax npm
package](https://www.npmjs.com/package/mathjax) (the source code is
included in the [mathjax-full npm
package](https://www.npmjs.com/package/mathjax-full)).
### Key Branches & Tags
MathJax uses several permanent branches in the [MathJax source repository](https://github.com/mathjax/MathJax-src):
- **[develop](https://github.com/mathjax/MathJax-src/tree/develop)**
is the development branch. All work on the next release happens here
so you should generally branch off `develop` if you are going to
submit a pull request. Do **NOT** use this branch for a production
site.
- **[master](https://github.com/mathjax/MathJax-src)** contains the latest
release of MathJax. This branch may be used in production. Do
**NOT** use this branch to work on MathJax's source.
These branches reflect version 3 of MathJax, which is substantially
different from the version 2 codebase. Version 2 will continue to be
maintained while web sites transition to version 3, with work being
done using the following branches in the [MathJax distribution
repository](https://github.com/mathjax/MathJax):
- **[legacy-v2-develop](https://github.com/mathjax/MathJax/tree/legacy-v2-develop)**
is the development branch for changes to the legacy version 2 code.
Any pull requests for version 2 should be branched from here. Do
**NOT** use this branch for a production site.
- **[legacy-v2](https://github.com/mathjax/MathJax/tree/legacy-v2)**
is the branch that contains any updates to version 2 following
the release of version 3. Do **NOT** use this branch to work on
MathJax's source.
In addition to these branches, MathJax uses tags to identify the
various versions. These can be checked out to obtain the specified
release; for example, `git checkout 2.7.5` would get you the files for
version 2.7.5 of MathJax.
Note that version 3 is written in Typescript, and so must be compiled
to obtain usable javascript files, and that the components need to be
built once that is done. See the
[documentation](https://docs.mathjax.org/en/latest/web/hosting.html#getting-mathjax-via-git)
for details. For version 2, the source javascript files are not
compressed until a release is made, so you should use the copies in
the `unpacked` directory during development.
### Submitting Pull Requests
Pull requests are welcome. If you're looking to submit a PR for
something that doesn't have an open issue, please consider [raising an
issue](#reporting-an-issue) that your PR can close, especially if
you're fixing a bug. This makes it more likely that there will be
enough information available for your PR to be properly tested and
merged.
##### Need Help?
If you're not completely clear on how to submit/update/*do* Pull
Requests, please check out our [source control
policies](https://github.com/mathjax/MathJax/wiki/Source-control-policies). For
more insights, check the excellent in depth [Git Workflow
guide](https://github.com/TryGhost/Ghost/wiki/Git-Workflow) from
Ghost, in particular
* [Ghost Workflow guide: commit messages](https://github.com/TryGhost/Ghost/wiki/Git-workflow#commit-messages)
### Testing and Quality Assurance
If you're
looking to get involved with the code base and don't know where to
start, checking out and testing a pull request is one of the most
useful things you could do.
These are some [excellent
instructions](https://gist.github.com/piscisaureus/3342247) on
configuring your GitHub repository to allow you to checkout pull
requests in the same way as branches.
### Writing documentation
MathJax's main documentation can be found at [docs.mathjax.org](http://docs.mathjax.org).
The source of the docs is hosted in the
[mathjax/MathJax-docs](http://github.com/mathjax/MathJax-docs) repo here on GitHub.
The documentation is generated using
[Sphinx-doc](http://sphinx-doc.org/) and hosted on [Read the
docs](http://readthedocs.org). You can clone the repo and submit pull
requests following the [pull-request](#submitting-pull-requests)
guidelines.
### Translation
If you wish to add or update translations of MathJax, please do it on
[TranslateWiki.net](https://translatewiki.net/w/i.php?title=Special:Translate&group=out-mathjax-0-all)
(and while you're there you can help other open source projects,
too).
For bug reports and other questions that don't fit on
TranslateWiki.net, head over to the
[mathjax/mathjax-i18n](https://github.com/mathjax/MathJax-i18n)
repository.
The translation files currently are for version 2, as localization
hasn't been added to version 3 yet.
## Conduct
As a NumFOCUS fiscally sponsored project, MathJax is governed by the
[NumFOCUS code of conduct](https://numfocus.org/code-of-conduct),
which we summarize as follows:
We are committed to providing a friendly, safe and welcoming
environment for all, regardless of gender, sexual orientation,
disability, ethnicity, religion, or similar personal characteristic.
Please be kind and courteous. There's no need to be mean or rude.
Respect that people have differences of opinion and that every design
or implementation choice carries a trade-off and numerous costs. There
is seldom a right answer, merely an optimal answer given a set of
values and circumstances.
Please keep unstructured critique to a minimum. If you have solid
ideas you want to experiment with, make a fork and see how it works.
We will exclude you from interaction if you insult, demean or harass
anyone. That is not welcome behaviour. We interpret the term
"harassment" as including the definition in the [Unacceptable
Behavior](https://numfocus.org/code-of-conduct#unacceptable-behavior)
section of the [NumFOCUS code of
conduct](https://numfocus.org/code-of-conduct); if you have any lack
of clarity about what might be included in that concept, please read
that definition. In particular, we don't tolerate behavior that
excludes people in socially marginalized groups.
Private harassment is also unacceptable. No matter who you are, if you
feel you have been or are being harassed or made uncomfortable by a
community member, please contact one of the channel ops or any of the
[MathJax](https://github.com/MathJax/MathJax) core team
immediately. Whether you're a regular contributor or a newcomer, we
care about making this community a safe place for you and we've got
your back.
Likewise any spamming, trolling, flaming, baiting, or other
attention-stealing behaviour is not welcome.
We also recommend that you read [discourse's