Line too long (alchemistry#424)

* docs\conf.py  line-too-long

Made line shorter, its end wasn't readable

* src\alchemlyb\visualisation\dF_state.py  too-many-branches

Function plot_dF_state had 42 branches, while it is recommended not to have more than 12.

The function is structured with clear blocks by logic and documentation.
I extracted methods to encapsulate the logical blocks, reducing complexity.

* src\alchemlyb\workflows\abfe.py  too-many-branches

Both methods generate_result and estimate had a bit too many branches.
I extracted methods to reduce complexity and make code clearer.

* src\alchemlyb\parsing\namd.py  too-many-branches

Two functions, extract_u_nk and _get_lambdas had too many branches. Smaller functions were extracted.

* src\alchemlyb\parsing\amber.py  line-too-long

Made two readable lines shorter

* src\alchemlyb\parsing\util.py   line-too-long

Made a readable line shorter

* src\alchemlyb\visualisation\ti_dhdl.py  too-many-statements

The function plot_ti_dhdl had 81 statements, while it is recommended not to have more than 50.
I extracted few smaller functions, reducing the length and increasing structure.

* Add default value for mnb in get_determine_orientation

The value of mnb is not set in the case of landscape orientation.
It was like that even before extracting get_determine_orientation.
However, now that this is a separated function, the test fails due to returning an unset variable.

This might detect a bigger bug regarding not setting it unintentionally.

* Fix _fit_estimators extraction

_fit_estimators
fails on
E       UnboundLocalError: cannot access local variable 'u_nk' where it is not associated with a value

Since the goal is to reduce branches I revert that and extract the more isolated check_estimators_availability instead

* Revert "Fix _fit_estimators extraction"

This reverts commit f017972.

* Revert "Add default value for mnb in get_determine_orientation"

This reverts commit a1ea9d9.

* Revert "src\alchemlyb\visualisation\ti_dhdl.py  too-many-statements"

This reverts commit d2ed7fa.

* Revert "src\alchemlyb\parsing\namd.py  too-many-branches"

This reverts commit 7ece0f8.

* Revert "src\alchemlyb\workflows\abfe.py  too-many-branches"

This reverts commit ea1ecca.

* Revert "src\alchemlyb\visualisation\dF_state.py  too-many-branches"

This reverts commit 3a311d4.

---------

Co-authored-by: Zhiyi Wu <zwu@exscientia.ai>

docs/conf.py

@@ -54,7 +54,8 @@
 # General information about the project.
 now = datetime.datetime.now()
 project = "alchemlyb"
-author = 'The alchemlyb development team (see <a href="https://raw.githubusercontent.com/alchemistry/alchemlyb/master/AUTHORS">AUTHORS</a>)'
+author = 'The alchemlyb development team ' \
+    + '(see <a href="https://raw.githubusercontent.com/alchemistry/alchemlyb/master/AUTHORS">AUTHORS</a>)'
 copyright = f"2017-{now.year}, " + author
 
 

src/alchemlyb/parsing/amber.py

@@ -334,15 +334,17 @@ def extract(outfile, T):
                 if nstep != old_nstep and dvdl is not None and nstep is not None:
                     if finished:
                         raise ValueError(
-                            "TI Energy detected after the TIMINGS section. Did you concatenate the output file?"
+                            "TI Energy detected after the TIMINGS section."
+                            + " Did you concatenate the output file?"
                         )
                     file_datum.gradients.append(dvdl)
                     nensec += 1
                     old_nstep = nstep
             elif line.startswith("MBAR Energy analysis") and file_datum.have_mbar:
                 if finished:
                     raise ValueError(
-                        "MBAR Energy detected after the TIMINGS section. Did you concatenate the output file?"
+                        "MBAR Energy detected after the TIMINGS section."
+                        + " Did you concatenate the output file?"
                     )
                 mbar = secp.extract_section(
                     "^MBAR", "^ ---", file_datum.mbar_lambdas, extra=line

src/alchemlyb/parsing/util.py

@@ -78,7 +78,8 @@ def anyopen(datafile: Union[PathLike, IO], mode="r", compression=None):
             return compressor(datafile, mode=mode)
         else:
             raise ValueError(
-                "`datafile` is a stream, but specified `compression` '{compression}' is not supported"
+                "`datafile` is a stream"
+                + ", but specified `compression` '{compression}' is not supported"
             )
 
     # otherwise, treat as a file