make example env file when running cellpy setup

cellpy/cli.py

@@ -96,6 +96,12 @@ def save_prm_file(prm_filename):
     prmreader._write_prm_file(prm_filename)
 
 
+def dump_env_file(env_filename):
+    """saves (writes) the env to file"""
+    print("dumping env file to", env_filename)
+    prmreader._write_env_file(env_filename)
+
+
 def get_package_prm_dir():
     """gets the folder where the cellpy package lives"""
     return pathlib.Path(cellpy.parameters.__file__).parent
@@ -228,6 +234,7 @@ def setup(
     # generate variables
     init_filename = prmreader.create_custom_init_filename()
     user_dir, dst_file = prmreader.get_user_dir_and_dst(init_filename)
+    env_file = prmreader.get_env_file()
 
     if dry_run:
         click.echo("Create custom init filename and get user_dir and destination")
@@ -262,6 +269,9 @@ def setup(
         click.echo(f"[cellpy] {dst_file} not found -> I will make one for you!")
         reset = True
 
+    if not pathlib.Path(env_file).is_file():
+        click.echo(f"[cellpy] {env_file} not found -> I will make one, but you must edit it yourself!")
+
     if interactive:
         click.echo(" interactive mode ".center(80, "-"))
         _update_paths(
@@ -273,6 +283,7 @@ def setup(
             interactive=True,
         )
         _write_config_file(user_dir, dst_file, init_filename, dry_run)
+        _write_env_file(user_dir, env_file, dry_run)
         _check(dry_run=dry_run)
 
     else:
@@ -287,6 +298,7 @@ def setup(
                 silent=silent,
             )
         _write_config_file(user_dir, dst_file, init_filename, dry_run)
+        _write_env_file(user_dir, env_file, dry_run)
         _check(dry_run=dry_run)
 
 
@@ -768,6 +780,36 @@ def _write_config_file(user_dir, dst_file, init_filename, dry_run):
         )
 
 
+def _write_env_file(user_dir, dst_file, dry_run):
+    click.echo(" update configuration ".center(80, "-"))
+    click.echo("[cellpy] (setup) Writing environment file:")
+    click.echo(f"\n         {user_dir}\n")
+
+    if os.path.isfile(dst_file):
+        click.echo(f"[cellpy] (setup) Environment file {dst_file} already exists!")
+        return
+
+    try:
+        if dry_run:
+            click.echo(
+                f"*** dry-run: skipping actual saving of {dst_file} ***", color="red"
+            )
+        else:
+            click.echo(f"[cellpy] (setup) Saving file ({dst_file})")
+            dump_env_file(dst_file)
+
+    except ConfigFileNotWritten:
+        _txt = "[cellpy] (setup) No, that did not work either.\n"
+        _txt += "[cellpy] (setup) Well, guess you have to talk to the developers."
+        click.echo(_txt)
+    else:
+        click.echo(f"[cellpy] (setup) Environment file written!")
+        click.echo(
+            f"[cellpy] (setup) OK! Now you can edit it. For example by "
+            f"issuing \n\n         [your-favourite-editor] {init_filename}\n"
+        )
+
+
 def _get_default_editor():
     """
     Return the default text editor.

cellpy/parameters/.cellpy_prms_default.conf

@@ -96,6 +96,7 @@ Reader:
   capacity_interpolation_step: 2.0
   use_cellpy_stat_file: false
   auto_dirs: true
+  jupyter_executable:
 Materials:
   cell_class: LIB
   default_material: silicon

cellpy/parameters/prmreader.py

@@ -27,6 +27,21 @@
 
 DEFAULT_FILENAME = DEFAULT_FILENAME_START + "default" + DEFAULT_FILENAME_END
 
+ENVIRONMENT_EXAMPLE = """
+# This is an example of an environment file for cellpy.
+# The environment file is used to set environment variables
+# that are used by cellpy.
+# The environment file should be located in the user directory
+# (i.e. the directory returned by pathlib.Path.home()).
+# The default environment file is named .env_cellpy, but you can
+# change this in your config file.
+# The environment file should contain the following variables:
+# CELLPY_PASSWORD=<password>
+# CELLPY_KEY_FILENAME=<key_filename>
+# CELLPY_HOST=<host>
+# CELLPY_USER=<user>
+"""
+
 # logger = logging.getLogger(__name__)
 
 yaml = YAML()
@@ -89,7 +104,7 @@ def get_user_dir():
 
 
 def _write_prm_file(file_name=None):
-    logging.debug("saving configuration to %s" % file_name)
+    logging.debug(f"saving configuration to {file_name}")
     config_dict = _pack_prms()
 
     try:
@@ -103,6 +118,24 @@ def _write_prm_file(file_name=None):
         raise ConfigFileNotWritten
 
 
+# TODO: make this alive by setting it to not dev:
+def _write_env_file(env_file_name=None):
+    """writes example environment file"""
+    dev = True
+    if env_file_name is None:
+        env_file_name = get_env_file_name()
+
+    logging.debug(f"saving environment arguments to {env_file_name}")
+    if dev:
+        print("---in-env-file------------------------------------")
+        print(ENVIRONMENT_EXAMPLE)
+        print("--------------------------------------------------")
+        return
+
+    with open(env_file_name, "w") as env_file:
+        env_file.write(ENVIRONMENT_EXAMPLE)
+
+
 def _update_prms(config_dict, resolve_paths=True):
     """updates the prms with the values in the config_dict"""
     # config_dict is your current config
@@ -331,7 +364,8 @@ def _save_current_prms_to_user_dir():
 
 def get_env_file_name():
     """returns the location of the env-file"""
-    return pathlib.Path(prms.Paths.env_file)
+    env_file = pathlib.Path(prms.Paths.env_file)
+    return env_file
 
 
 def info():

cellpy/parameters/prms.py

@@ -41,7 +41,7 @@ def keys(self):
         return self.__dataclass_fields__.keys()
 
 
-# If updating this, you will have to do a lot of tweaks.
+# If updating PathsClass, you will have to do a lot of tweaks.
 #   .cellpy_prms_default.conf
 #   cli.py (_update_paths)
 #   test_cli_setup_interactive (NUMBER_OF_DIRS)
@@ -135,6 +135,7 @@ class ReaderClass(CellPyConfig):
     auto_dirs: bool = (
         True  # v2.0 search in prm-file for res and hdf5 dirs in cellpy.get()
     )
+    jupyter_executable: str = "jupyter"
 
 
 @dataclass