Merge branch 'master' of https://github.com/DeDop/dedop-core

.github/issue_template.md

@@ -12,7 +12,7 @@
 
 ### Actual behavior
 
-*Describe here what you expected DeDop to do.*
+*Describe here what you observed.*
 
 ### Steps to reproduce the issue
 

README.md

@@ -42,7 +42,7 @@ type:
 
 If you want the environment to be installed in another location, e.g. due to disk space limitations, type:
 
-    $ conda env create --file environment.yml --prefix some/other/location/for/cate
+    $ conda env create --file environment.yml --prefix some/other/location/for/dedop
 
 Next step is to activate the new environment. On Linux/Darwin type:
 
@@ -53,11 +53,11 @@ Windows users can omit the `source` command and just type
 
     > activate dedop
 
-You can now safely install and run Cate sources into the new `dedop` environment.
+You can now safely install and run DeDop sources into the new `dedop` environment.
 
     (dedop) $ python setup.py develop
 
-To permanently install Cate into the Python environment (not recommended while in development mode!), type:
+To permanently install DeDop into the Python environment (not recommended while in development mode!), type:
 
     (dedop) $ python setup.py install
 
@@ -82,11 +82,11 @@ If you like to perform L1B product analysis tasks with DeDop using an IPython No
 
 The most up-to-date and complete list of module requirements is found in the project's `environment.yml` file.
 
-To install and run Cate from sources directly, type:
+To install and run DeDop from sources directly, type:
 
     $ python setup.py develop
 
-To permanently install Cate into Python (not recommended while in development mode!), type:
+To permanently install DeDop into Python (not recommended while in development mode!), type:
 
     $ python setup.py install
 

docs/user_manual.rst

@@ -6,6 +6,7 @@ User Manual
    :maxdepth: 1
 
    user_manual/um_setup
+   user_manual/um_ws_and_config_concept
    user_manual/um_shell
    user_manual/um_studio
 

docs/user_manual/um_setup.rst

@@ -2,13 +2,13 @@
 Setup
 ======
 
-Installation
-=============
+DeDop Shell Installation
+=========================
 
 From Binaries
 --------------
 
-DeDop is distributed as pre-compiled binaries which can be retrieved from `here <https://github.com/DeDop/dedop/releases/tag/v0.5.3>`_.
+DeDop is distributed as pre-compiled binaries which can be retrieved from `here <https://github.com/DeDop/dedop/releases/tag/v1.2.0>`_.
 For the windows Windows platforms there is a dedicated installer executable. For Mac OS and Unixes a ZIP file is provided.
 All platform distributions have a bundled Python interpreter, that's also the reason why they are quite large in size
 (roughly 300 megabytes).
@@ -50,3 +50,8 @@ After installing from source, you should be able to run the DeDop Shell, try::
 
     dedop --help
 
+
+DeDop Studio Installation
+==========================
+
+Information can be found in `this page <https://github.com/DeDop/dedop-studio>`_.

docs/user_manual/um_shell.rst

@@ -2,34 +2,31 @@
 DeDop Shell
 ============
 
+Overview
+========
+
 The DeDop tool set currently comprises the *DeDop Shell* - a command-line interface to the
 Delay Doppler Processor (DDP) - and *DeDop Studio* - a graphical user interface to the
 Delay Doppler Processor (DDP). In this section, you will find the manual for DeDop Shell.
 For the manual of DeDop Studio go to :doc:`um_studio`.
 
+The DeDop Shell comprises a single command-line executable, which is called ``dedop`` and is available after installing
+the DeDop Shell on your computer. See section :doc:`um_setup` for more information.
+
 
 .. _workspace_manag:
 
 Workspace Management
 ====================
 
-**Workspace** in DeDop Shell refers to a space in the file system in which all the requires parts for processing are located.
-They include source files, configurations, output files, as well as the Jupyter notebooks. It is possible to have multiple
-workspaces and by default they are located under ``$USER_DIR/.dedop/workspaces``.
-For example::
-
-   C:\\Users\\dummy_user\\.dedop\\workspaces  # Windows
-   /home/dummy_user/.dedop/workspaces         # Linux
-   /Users/dummy_user/.dedop/workspaces        # MacOS
-
 Add a new workspace
 --------------------
 
 When DeDop Shell runs for the first time, there is no workspace available. An automatic creation of default workspace can
 be triggered by running ``dedop input add some/path/to/your/L1A.nc`` or ``dedop run`` command as described
 :ref:`here <processing_l1a_l1b>`.
 
-Another (more recommended) way to add a new workspace is by running the following command::
+To add a new workspace is by running the following command::
 
    $ dedop w add workspace_name
 

docs/user_manual/um_studio.rst

@@ -3,7 +3,7 @@ DeDop Studio
 =============
 
 DeDop Studio is a desktop application with a primary aim of providing a user-friendly experience for processing L1A files.
-It was designed based on the already-existing DeDop Shell, so the behavior is almost the same with its command line counterpart.
+It was designed based on the already-existing :doc:`um_shell`, so the behavior is almost the same with its command line counterpart.
 
 .. figure:: ../_static/figures/dedop-studio.png
    :scale: 75%
@@ -107,7 +107,17 @@ To initiate a processing, click ``Run`` button inside **Processor Runs** panel.
 required parameters (input file, configuration, and output directory) have been selected. When any of them are missing,
 a dialog box will pop up with the information on which field you have to fill up. Otherwise, the processing will be started,
 marked by a new entry on the table. You can monitor the progress of the processing and at the moment, because the tool is
-capable only running one process at a time, the ``Run`` button is blocked as long as a process is running.
+capable only running one process at a time, the ``Run`` button is blocked, displayed as a spinner, as long as a process
+is running.
+
+In the end, a process can either be successful or fail. This status is indicated by the icon under ``Action`` column on
+the table in **Processor Runs** panel. On the image above, for example, the first three rows indicate that the processes
+are successful and when icon is clicked, the page will transition to screen 4,
+:ref:`Result & Analysis <analyse_l1b_studio>`. In the case of failure, mouse over on the icon to show a short description
+of the error as a tooltip text.
+
+When DeDop Studio is closed, the information in the table is preserved, by storing the data into ``dedop-prefs.json``.
+During the next startup of DeDop Studio, this information is loaded and used to populate the table.
 
 
 .. _analyse_l1b_studio:
@@ -119,4 +129,13 @@ Analysing L1B Results
    :scale: 75%
    :align: center
 
-
+The purpose of this screen is to manage what to do with the result products after a processing. There are two panels:
+Output Files and Analysis Configuration. In **Output Files**, users can navigate to different output files in the current
+workspace directory, grouped by configurations. By clicking a file name, the said file is selected. This has an implication
+on which actions are available, depending on how many files are selected. If only one file is selected, the ``Inspect``
+button on **Analysis Configuration** panel is enabled. When two files are selected, the ``Compare`` button is enabled.
+Clicking one of these buttons will trigger a creation of a Jupyter notebook suitable for inspecting or comparing the
+file(s) that have been selected, and to start a local instance of Jupyter notebook server. This behavior is consistent
+with DeDop Shell command :ref:`dedop output compare/inspect <analyse_l1b>`. The dropdown list at the bottom of
+**Analysis Configuration** is used to select a notebook file that has been previously created through ``Inspect`` and
+``Compare`` buttons.

docs/user_manual/um_ws_and_config_concept.rst

@@ -0,0 +1,53 @@
+===================================
+Workspace and Configuration Concept
+===================================
+
+Workspace
+==========
+
+**Workspace** in DeDop Shell refers to a space in the file system in which all the requires parts for processing are located.
+They include source files, configurations, output files, as well as the Jupyter notebooks. It is possible to have multiple
+workspaces and by default they are located under ``$USER_DIR/.dedop/workspaces``.
+For example::
+
+   C:\\Users\\dummy_user\\.dedop\\workspaces  # Windows
+   /home/dummy_user/.dedop/workspaces         # Linux
+   /Users/dummy_user/.dedop/workspaces        # MacOS
+
+When DeDop Shell runs for the first time, there is no workspace available. An automatic creation of default workspace can
+be triggered by running ``dedop input add some/path/to/your/L1A.nc`` or ``dedop run`` command as described
+:ref:`here <processing_l1a_l1b>`.
+
+Another (more recommended) way to add a new workspace is by running the following command::
+
+   $ dedop w add workspace_name
+
+Upon successful operation, the following responses shall be returned::
+
+   created workspace "workspace_name"
+   current workspace is "workspace_name"
+
+This means that the new workspace has been successfully created and made the current workspace, which means that, unless
+explicitly changed, whatever operations being performed after this will happen inside this workspace.
+
+Inside ``workspaces`` directory, there is a file called ``.current``, inside which the name of the current workspace can
+be found. When there is no current workspace (eg. because there is no more workspace after a deletion), this file will
+be empty.
+
+More information and example on workspace management operations, please go to :ref:`here <workspace_manag>`.
+
+Configuration
+==============
+
+**DeDop configuration** refers to a set of configurations (Configuration, Characterization, Constants), which in the file
+system are stored as CNF.json, CHD.json, and CST.json. Most of the time, users will need to modify only the **Configuration**.
+A configuration is represented by a directory with a name of the configuration name and is located under ``configs``
+directory inside a workspace directory. It is possible to have multiple configurations under each workspace and it is
+recommended to have a new configuration for different set of configuration values. This way, an output can be easily reproduced
+if needed in the future.
+
+As in ``workspaces`` directory, there is a ``.current`` file inside ``configs`` directory. It works following exactly the same
+concept: this file has the information on what is the current configuration. In the case of no current configuration,
+this file will be empty.
+
+More information and example on configuration management operations, please go to :ref:`here <config_manag>`.

tests/webapi/test_websocket.py

@@ -83,8 +83,8 @@ def test_config_management(self):
         self.assertIn('chd', sentinel_configs)
         self.assertIsInstance(sentinel_configs['chd'], dict)
         self.assertEqual(len(sentinel_configs['chd']), 13)
-        self.assertEqual(sentinel_configs['chd']['mean_sat_alt_chd']['value'], 815000.0)
-        self.assertEqual(sentinel_configs['chd']['brf_sar_chd']['value'], 78.52)
+        self.assertEqual(sentinel_configs['chd']['mean_sat_alt_chd']['value'], 814500.0)
+        self.assertEqual(sentinel_configs['chd']['brf_sar_chd']['value'], 78.53069)
         self.assertIn('cnf', sentinel_configs)
         self.assertIsInstance(sentinel_configs['cnf'], dict)
         self.assertEqual(len(sentinel_configs['cnf']), 25)