chore(dependencies/docs): update conda env, fix notebooks (#2414)

The `environment.yml` was missing a few optional/developer dependencies we've recently added to `pyproject.toml`. Bring the former into sync with the latter (and list packages in the same order).

With luck, conda will eventually be able to consume `pyproject.toml` files, and we can remove `environment.yml`. More info at issue 10633 on the conda repo (not linking to avoid the crossref showing up there).

There were some old pycharm cell format comments in the notebook scripts which jupytext didn't like, remove them.

This should close #2253. To avoid similar situations in the future, don't skip notebooks due to missing dependencies in CI. We did this for convenient local testing, so tests can run without all optional dependencies, but CI should be strict.

.docs/Notebooks/array_output_tutorial.py

@@ -17,16 +17,13 @@
 #       - name: Jeremy White
 # ---
 
-# + [markdown] pycharm={"name": "#%% md\n"}
 # # Formatting ASCII output arrays
 #
 # ### Configuring numeric arrays written by FloPy
 
-# + [markdown] pycharm={"name": "#%% md\n"}
 # load and run the Freyberg model
 
 
-# + pycharm={"name": "#%%\n"}
 import os
 import sys
 from pathlib import Path
@@ -111,26 +108,20 @@
         errmsg = f"Error. Output file cannot be found: {f}"
         print(errmsg)
 
-# + [markdown] pycharm={"name": "#%% md\n"}
 # Each ``Util2d`` instance now has a ```.format``` attribute, which is an ```ArrayFormat``` instance:
 
-# + pycharm={"name": "#%%\n"}
 print(ml.lpf.hk[0].format)
 
-# + [markdown] pycharm={"name": "#%% md\n"}
 # The ```ArrayFormat``` class exposes each of the attributes seen in the ```ArrayFormat.___str___()``` call. ```ArrayFormat``` also exposes ``.fortran``, ``.py`` and ``.numpy`` atrributes, which are the respective format descriptors:
 
-# + pycharm={"name": "#%%\n"}
 print(ml.dis.botm[0].format.fortran)
 print(ml.dis.botm[0].format.py)
 print(ml.dis.botm[0].format.numpy)
 
-# + [markdown] pycharm={"name": "#%% md\n"}
 # #### (re)-setting ```.format```
 #
 # We can reset the format using a standard fortran type format descriptor
 
-# + pycharm={"name": "#%%\n"}
 ml.dis.botm[0].format.free = False
 ml.dis.botm[0].format.fortran = "(20f10.4)"
 print(ml.dis.botm[0].format.fortran)
@@ -147,25 +138,19 @@
 else:
     raise ValueError("Failed to run.")
 
-# + [markdown] pycharm={"name": "#%% md\n"}
 # Let's load the model we just wrote and check that the desired ```botm[0].format``` was used:
 
-# + pycharm={"name": "#%%\n"}
 ml1 = flopy.modflow.Modflow.load("freyberg.nam", model_ws=modelpth)
 print(ml1.dis.botm[0].format)
 
-# + [markdown] pycharm={"name": "#%% md\n"}
 # We can also reset individual format components (we can also generate some warnings):
 
-# + pycharm={"name": "#%%\n"}
 ml.dis.botm[0].format.width = 9
 ml.dis.botm[0].format.decimal = 1
 print(ml1.dis.botm[0].format)
 
-# + [markdown] pycharm={"name": "#%% md\n"}
 # We can also select ``free`` format.  Note that setting to free format resets the format attributes to the default, max precision:
 
-# + pycharm={"name": "#%%\n"}
 ml.dis.botm[0].format.free = True
 print(ml1.dis.botm[0].format)
 # -
@@ -178,6 +163,5 @@
 else:
     raise ValueError("Failed to run.")
 
-# + pycharm={"name": "#%%\n"}
 ml1 = flopy.modflow.Modflow.load("freyberg.nam", model_ws=modelpth)
 print(ml1.dis.botm[0].format)

.docs/Notebooks/mt3dms_sft_lkt_uzt_tutorial.py

@@ -841,7 +841,6 @@
 
 # #### Write the MT3D-USGS input files for inspecting and running
 
-# + pycharm={"name": "#%%\n"}
 mf.write_input()
 mt.write_input()