Merge pull request #14 from HealthyPear/update-CHANGELOG_and_README

Updated CHANGELOG and README for 0.2 release (Closes #4)

CHANGELOG.md

@@ -1,68 +1,48 @@
 <ins>Author:</ins> Dr. Michele Peresano  
-<ins>Affiliation:</ins> CEA-Saclay / Irfu
+<ins>Affiliation:</ins> CEA-Saclay / Irfu / DAp
 
-# What's new
+#### Contributors in alphabetical order
 
-## October 4th, 2019
+- Alice Donini
+- Karl Kosack
+- Thierry Stolarczyk
+- Michele Peresano
+- Thomas Vuillaume
 
-### General changes
+# Releases
 
- - Removed explicit dependencies from the environment file: these were interfacing with C++ libraries with different names which were preventing cross-platform installation,
- - Updated README.
+## [0.2](https://github.com/cta-observatory/protopipe/compare/v0.1.1...0.2) (Oct 23rd, 2019)
 
-## October 4th, 2019
+_protopipe_ 0.2 now fully supports the stable release of _ctapipe_ 0.7.0. The main improvements involve the calibration process (high gain selected by default), the direction reconstruction and new camera-type labels.
 
-### General changes
+Code based on _pywi_/_pywi-cta_ libraries, relevant for wavelet-based image cleaning, has been removed in favor of _ctapipe_ or made completely optional where needed. Wavelet cleaning is still optional but will need those two libraries to be additionally installed. Tailcut-based cleaning is now faster.
 
- - Fixed environment file containing specific macos-dependent package builds, which were preventing a smooth installation on a Linux machine,
- - Updated README.
+The README has been improved with installation, basic use, and developer instructions. Dependencies are listed in `protopipe_environment.yaml` and have been simplified.
 
-## October 2nd, 2019
+The auxiliary scripts `merge_tables.py` and `merge.sh` have been added to allow merging of DL1 and DL2 HDF5 tables.
 
-### Disclaimer(s)
+The `mars_cleaning_1st_pass` method is now imported from _ctapipe_. Novel code using the largest cluster of survived pixels (`number_of_islands` and `largest_island` methods in the `event_preparer` module) has been hardcoded in _protopipe_ and will disappear with the next release of _ctapipe_.
 
- - For the moment, the master branch host code almost completely compliant with ctapipe 0.7.
- - It is currently been tested
-   - Expect potentially frequent changes.
-   - Use it and fell free to comment / communicate any strange or wrong behaviour
- - Expect a more organized approach to the development with reviewed pull-requests.
+Model estimators now load the camera types directly from the `analysis .yaml` configuration file.
 
-### General changes
+### Pull Requests:
 
-- Almost complete support for ctapipe 0.7
-  - 1D to 2D conversion of DL1 images is still done using pywi-cta
-- PEP8 compliant formatting through the whole code
-- Removed some stale commented code
-- README.rst has been updated "Requirements" and a new "Basic use" instruction section
-- Added auxiliary scripts which allow to merge DL1 and DL2 HDF5 tables
+This is an incomplete list: only notable entries are listed.
 
-### Specific changes
+- [[#13](https://github.com/cta-observatory/protopipe/pull/13)] Bugfix in `save_fig` method used by `model_diagnostic.py`
+- [[#10](https://github.com/cta-observatory/protopipe/pull/10)] Update installation process
+- [[#9](https://github.com/cta-observatory/protopipe/pull/9)] Update image cleaning and make wavelet-based algorithms independent
+- [[#8](https://github.com/cta-observatory/protopipe/pull/8)] Import CTA-MARS 1st pass cleaning from ctapipe
 
-* scripts/write_dl1.py
-  - now only one DL1 calibrated image is (optionally) saved, since ctapipe 0.7 choses the gain autonomously
-  - Updated LST and MST camera type keys
-* scripts/write_dl2.py
-  - as in write_dl1.py, only one DL1 calibrated image is (optionally) saved
-  - Estimator files now loaded using camera types read directly from analysis configuration file
-* pipeline/event_preparer.py
-  - updated calibration process with support for ctapipe 0.7
-  - updated direction reconstruction with support for ctapipe 0.7
-  - dumped the use of pywi-cta in obtaining the calibrated image in favor of ctapipe
-  - Updated LST and MST camera type keys
+## [0.1.1](https://github.com/cta-observatory/protopipe/compare/v0.1...0.1.1) (Oct 1st, 2019)
 
-# Previous releases
+The `write_dl1` and `write_dl2` tools can now save an additional file through the flag `--save-images` when applied to a single run. This file will contain the original and calibrated (after gain selection) photoelectron images per event.
 
-<ins>protopipe 0.1.1:</ins>
+A new method `save_fig` has been introduced in the `utils` module, so that `model_diagnostic` can save images also in PNG format.
 
-* scripts/write_dl1.py
-  - added optional saving of images of a run in separate file for test purposes
-* scripts/write_dl2.py
-  - added optional saving of images of a run in separate file for test purposes
-* pipeline/event_preparer.py
-  - added support for the optional storage of DL1 images
-* scripts/model_diagnostic.py
-  - added import of new pipeline/utils.py function "save_fig" and applied it
-  - PEP8 formatting via "black" package
-* pipeline/utils.py
-  - added function "save_fig" to save figures in multiple formats
-  - added docstring to "load_config"
+Additional docstrings and PEP8 formatting have been added throughout the code.
+
+## 0.1 (Sep 23rd, 2019)
+
+This version of protopipe is based on ctapipe 0.6.2 (conda package stable version).
+Its performance has been [shown](https://indico.cta-observatory.org/event/1995/contributions/19991/attachments/15559/19825/CTAC_Lugano_2019_Peresano.pdf) at the CTAC meeting in Lugano 2019.

README.md

@@ -78,10 +78,18 @@ Instructions for developers:
 1. Fork the master _protopipe_ remote repository as explained [here](https://help.github.com/en/articles/fork-a-repo)
 2. Follow the installation instructions above, but using __your__ remote repository (we'll call __origin__ yours and __upstream__ the official one)
 3. if you want to develop something new:
-    1. create a new branch from your __local__ _master_ branch
-    2. develop inside it
-    3. push it to __origin__
-    4. continue to develop and push until you feel ready
+    1. update __local__ _master_ branch (`git pull upstream master`)
+    3. create a new branch from your __local__ _master_ branch
+    4. develop inside it
+    5. push it to __origin__
+    6. continue to develop and push until you feel ready
 4. start a __pull request__ from __origin/your_branch__ to __upstream/master__
     1. wait for an outcome
     2. if necessary, you can update or fix things in your branch because now everything is traced (__local/your_branch__ --> __origin/your_branch__ --> __pull request__)
+
+_**Note:**_ if your developments take a relatively long time,
+
+1. update periodically your __local__ _master_ branch,
+2. if updates have been made, go to your __local__ _development_ branch (`git checkout your_branch`)
+3. if there are no conflicts, move the beginning of your branch at the end of the updated master (`git rebase master`)
+4. push your branch to your remote