WIP: update README

README.rst

@@ -18,12 +18,28 @@ Installation instructions
 =========================
 * Go to the directory where you want the Python code to be installed and simply download it or clone it via *git* as::
 
-  >>> git clone https://github.com/SNflows/flows.git .
+  >>> git clone https://github.com/SNflows/flows.git
+  >>> cd flows
 
 * Required dependencies can be installed using the following command. It is recommended to do this in a dedicated `virtualenv <https://virtualenv.pypa.io/en/stable/>`_ or similar:
 
+  >>> python3 -m venv env
+  >>> source env/bin/activate
+  >>> pip install --upgrade pip
   >>> pip install -r requirements.txt
-  >>> pip install -r requirements_dev.txt  # for tests/development
+
+* In addition, in order to run tests and do development, do
+
+  >>> pip install -r dev_requirements.txt  # in same virtual environment as above
+  >>> _pyver=$(find env/lib/ -type d -mindepth 1 -maxdepth 1 | cut -d '/' -f 3)
+  >>> ln -s ../env/lib/${_pyver}/site-packages/tendrils/utils/config.ini flows/config.ini
+  >>> wget -O tests/input/2020aatc/SN2020aatc_K_20201213_495s.fits.gz https://anon.erda.au.dk/share_redirect/FJGx69KFvg
+  >>> wget -O tests/input/2020lao/59000.96584_h_e_20200531_33_1_1_1_2020lao_LT_gp.fits.gz https://anon.erda.au.dk/share_redirect/E98lmqOVWf
+  >>> wget -O tests/input/2020lao/subtracted/59000.96584_h_e_20200531_33_1_1_1_2020lao_LT_gpdiff.fits.gz https://anon.erda.au.dk/share_redirect/bIxyzrRXbg
+  >>> wget -O tests/input/2021wyw/ADP.2021-10-15T11_40_06.553.fits.gz https://anon.erda.au.dk/share_redirect/Gr8p2K7ph5
+
+
+TODO: Reformulate following bullet point and check/decide on which config paths are/should be available...:
 
 * **Changed with ``tendrils`` API.** If using ``tendrils``, follow the steps below, but then let ``tendrils`` know of the config file location. Alternatively, individual config file elements can be set programatically using `tendrils` and will be saved to a config file automatically. Last step is to create a config-file. Create a file named "config.ini" and place it in the "flows" directory. Make sure that the file can only be read by you (``chmod 0600 config.ini``)!
   This file can contain all the settings for running the pipeline. A minimal file for working with the pipeline is
@@ -36,7 +52,7 @@ Installation instructions
       [TNS]
       api_key = <AUFLOWS_BOT API key>
 
-  Where your API token can be found on the Flows webpage. 
+  Where your API token can be found on the Flows webpage.
 
 
 How to run tests
@@ -51,34 +67,85 @@ Text coming soon...
 
 .. code-block:: ini
 
-    [api]
-    token =
-    photometry_cache =
-
-    [photometry]
-    archive_local =
-    output =
+    ##########################################################
+    ### --Tendrils configurations used at FLOWS run-time-- ###
+    ### Configurations without a leading '#' are required  ###
+    ### and must be specified by the user.                 ###
+    ### Configurations with a leading '#' are optional,    ###
+    ### and their assigned values are documentation of     ###
+    ### their default values in the FLOWS pipeline.        ###
+    ### Default values of optional configurations with a   ###
+    ### leading '$' signify environment variables resolved ###
+    ### at run-time; their fallbacks are given following   ###
+    ### a '/'.                                             ###
+    ##########################################################
 
+    [api]
+    # photometry_cache = None
+    # pipeline = False
+    token = None
+
+    # casjobs:
+    #   wsid and password required for run_catalogs.py,
+    #   user registration at
+    #   https://galex.stsci.edu/casjobs/CreateAccount.aspx
+    #   wsid can be found at
+    #   https://galex.stsci.edu/casjobs/changedetails.aspx
+    #   after login
     [casjobs]
-    wsid =
-    password =
+    # wsid = $CASJOBS_WSID/None
+    # password = $CASJOBS_PASSWORD/None
+
+    # database:
+    #   username and password required for run_catalogs.py,
+    #   the user is a registered user in the flows database
+    #   with access to the 'adastra' schema
+    [database]
+    # username = $AUDBUsername/None
+    # password = $AUDBPassword/None
 
+    [photometry]
+    archive_local = None
+    # output = .
+
+    # TNS:
+    #   api_key required for run_querytns.py,
+    #   user registration at
+    #   https://www.wis-tns.org/user
+    #   api_key is that of a TNS bot; ask a flows group
+    #   member for one
+    #   if user_id and user_name are not given, fallback
+    #   to a TNS bot's bot_id and bot_name, which must
+    #   match with api_key
     [TNS]
-    api_key =
-    bot_id =
-    bot_name =
-    user_id =
-    user_name =
+    # api_key = None
+    # bot_id = 191396
+    # bot_name = AUFLOWS_BOT2
+    # user_id = None
+    # user_name = None
+
+    [URL]
+    # base_url = https://flows.phys.au.dk/api/
+    # catalogs_url = reference_stars.php
+    # catalogs_missing_url = catalog_missing.php
+    # cleanup_photometry_status_url = cleanup_photometry_status.php
+    # datafiles_url = datafiles.php
+    # filters_url = filters.php
+    # lightcurves_url = lightcurve.php
+    # photometry_upload_url = upload_photometry.php
+    # photometry_url = download_photometry.php
+    # set_photometry_status_url = set_photometry_status.php
+    # sites_url = sites.php
+    # targets_post_url = targets_add.php
+    # targets_url = targets.php
+    # verify_ssl = True
 
     [ztf]
-    output_photometry =
+    # output_photometry = .
 
-    [database]
-    username =
-    password =
 
-Making a release      
-================     
+Making a release
+================
 
  - Bump sem-version when Devel is ready to merge in file = VERSION (v1.0.0). Checkout devel. Edit Version. Push devel.
  - Merge Devel into Master (Create PR from Devel -> Master), wait until tests are passing. Create issues if not. Then Merge.