Update dev docs

Author: shyuep

docs/custodian.ansible.interpreter.md

@@ -36,7 +36,7 @@ Examples:
 Initializes a Modder from a list of supported actions.
 
 * **Parameters**
-  * **actions** ( *[**Action**]*) – A sequence of supported actions. See
+  * **actions** (  *[**Action**]*) – A sequence of supported actions. See
     [`custodian.ansible.actions`](custodian.ansible.actions.md#module-custodian.ansible.actions). Default is None,
     which means only DictActions are supported.
   * **strict** (*bool*) – Indicating whether to use strict mode. In non-strict

docs/custodian.cp2k.interpreter.md

@@ -20,7 +20,7 @@ Initializes a Modder for Cp2kInput sets
 * **Parameters**
   * **filename** (*str*) – name of cp2k input file to modify. This file will be overwritten
     if actions are applied.
-  * **actions** ( *[**Action**]*) – A sequence of supported actions. See
+  * **actions** (  *[**Action**]*) – A sequence of supported actions. See
     [`custodian.ansible.actions`](custodian.ansible.actions.md#module-custodian.ansible.actions). Default is None,
     which means DictActions and FileActions are supported.
   * **strict** (*bool*) – Indicating whether to use strict mode. In non-strict

docs/custodian.cp2k.jobs.md

@@ -37,7 +37,7 @@ of the static constructors. The defaults are usually fine too.
   * **backup** (*bool*) – Whether to backup the initial input files. If True,
     the input file will be copied with a
     “.orig” appended. Defaults to True.
-  * **settings_override** ( *[**actions**]*) – A list of actions. See the Cp2kModder
+  * **settings_override** (  *[**actions**]*) – A list of actions. See the Cp2kModder
     in interpreter.py
   * **restart** (*bool*) – Whether to run in restart mode, i.e. this a continuation of
     a previous calculation. Default is False.

docs/custodian.custodian.md

@@ -52,11 +52,11 @@ every 30 x 10 = 300 seconds, i.e., 5 minutes. -->
 Initializes a Custodian from a list of jobs and error handlers.
 
 * **Parameters**
-  * **handlers** ( *[**ErrorHandler**]*) – Error handlers. In order of priority of
+  * **handlers** (  *[**ErrorHandler**]*) – Error handlers. In order of priority of
     fixing.
-  * **jobs** ( *[**Job**]*) – Sequence of Jobs to be run. Note that this can be
+  * **jobs** (  *[**Job**]*) – Sequence of Jobs to be run. Note that this can be
     any sequence or even a generator yielding jobs.
-  * **validators** ( *[**Validator**]*) – Validators to ensure job success
+  * **validators** (  *[**Validator**]*) – Validators to ensure job success
   * **max_errors_per_job** (*int*) – Maximum number of errors per job allowed
     before exiting. Defaults to None, which means it is set to be
     equal to max_errors..

docs/custodian.feff.interpreter.md

@@ -15,7 +15,7 @@ Bases: [`Modder`](custodian.ansible.interpreter.md#custodian.ansible.interpreter
 A Modder for FeffInput sets
 
 * **Parameters**
-  * **actions** ( *[**Action**]*) – A sequence of supported actions. See
+  * **actions** (  *[**Action**]*) – A sequence of supported actions. See
   * **actions** – A sequence of supported actions. See
     [`custodian.ansible.actions`](custodian.ansible.actions.md#module-custodian.ansible.actions). Default is None,
     which means DictActions and FileActions are supported.

docs/custodian.gaussian.handlers.md

@@ -41,17 +41,17 @@ Initialize the GaussianErrorHandler class.
     be monitored and plotted (convergence criteria versus cycle number) and
     saved to a file called ‘convergence.png’.
 
-### GRID_NAMES  *= (‘finegrid’, ‘fine’, ‘superfinegrid’, ‘superfine’, ‘coarsegrid’, ‘coarse’, ‘sg1grid’, ‘sg1’, ‘pass0grid’, ‘pass0’)*
+### GRID_NAMES   *= (‘finegrid’, ‘fine’, ‘superfinegrid’, ‘superfine’, ‘coarsegrid’, ‘coarse’, ‘sg1grid’, ‘sg1’, ‘pass0grid’, ‘pass0’)*
 
-### MEM_UNITS  *= (‘kb’, ‘mb’, ‘gb’, ‘tb’, ‘kw’, ‘mw’, ‘gw’, ‘tw’)*
+### MEM_UNITS   *= (‘kb’, ‘mb’, ‘gb’, ‘tb’, ‘kw’, ‘mw’, ‘gw’, ‘tw’)*
 
-### activate_better_guess  *= False*
+### activate_better_guess   *= False*
 
 ### check(directory: str = ‘./’)
 
 Check for errors in the Gaussian output file.
 
-### conv_criteria\*: ClassVar\*  *= {‘max_disp’: re.compile(’\\s+(Maximum Displacement)\\s+(-?\\d+.?\\d\*|.\*)\\s+(-?\\d+.?\\d\*)’), ‘max_force’: re.compile(’\\s+(Maximum Force)\\s+(-?\\d+.?\\d\*|.\*)\\s+(-?\\d+.?\\d\*)’), ‘rms_disp’: re.compile(’\\s+(RMS {5}Displacement)\\s+(-?\\d+.?\\d\*|.\*)\\s+(-?\\d+.?\\d\*)’), ‘rms_force’: re.compile(’\\s+(RMS {5}Force)\\s+(-?\\d+.?\\d\*|.\*)\\s+(-?\\d+.?\\d\*)’)}*
+### conv_criteria\*: ClassVar\*   *= {‘max_disp’: re.compile(’\\s+(Maximum Displacement)\\s+(-?\\d+.?\\d\*|.\*)\\s+(-?\\d+.?\\d\*)’), ‘max_force’: re.compile(’\\s+(Maximum Force)\\s+(-?\\d+.?\\d\*|.\*)\\s+(-?\\d+.?\\d\*)’), ‘rms_disp’: re.compile(’\\s+(RMS {5}Displacement)\\s+(-?\\d+.?\\d\*|.\*)\\s+(-?\\d+.?\\d\*)’), ‘rms_force’: re.compile(’\\s+(RMS {5}Force)\\s+(-?\\d+.?\\d\*|.\*)\\s+(-?\\d+.?\\d\*)’)}*
 
 ### *static* convert_mem(mem: float, unit: str)
 
@@ -71,13 +71,13 @@ Convert memory size between different units to megabytes (MB).
 
 Perform necessary actions to correct the errors in the Gaussian output.
 
-### error_defs\*: ClassVar\*  *= {‘A syntax error was detected in the input line.’: ‘syntax’, ‘Atom specifications unexpectedly found in input stream.’: ‘found_coords’, ‘Bad file opened by FileIO’: ‘bad_file’, ‘Convergence failure’: ‘scf_convergence’, ‘End of file in ZSymb’: ‘zmatrix’, ‘End of file reading connectivity.’: ‘coords’, ‘Error in internal coordinate system’: ‘internal_coords’, ‘FileIO operation on non-existent file.’: ‘missing_file’, ‘FormBX had a problem’: ‘linear_bend’, ‘Inv3 failed in PCMMkU’: ‘solute_solvent_surface’, ‘Linear angle in Tors.’: ‘linear_bend’, ‘No data on chk file.’: ‘empty_file’, ‘Optimization stopped’: ‘opt_steps’, ‘Out-of-memory error in routine’: ‘insufficient_mem’, ‘The combination of multiplicity ([0-9]+) and \\s+? ([0-9]+) electrons is impossible.’: ‘charge’, ‘There are no atoms in this input structure !’: ‘missing_mol’, ‘Z-matrix optimization but no Z-matrix variables.’: ‘coord_inputs’}*
+### error_defs\*: ClassVar\*   *= {‘A syntax error was detected in the input line.’: ‘syntax’, ‘Atom specifications unexpectedly found in input stream.’: ‘found_coords’, ‘Bad file opened by FileIO’: ‘bad_file’, ‘Convergence failure’: ‘scf_convergence’, ‘End of file in ZSymb’: ‘zmatrix’, ‘End of file reading connectivity.’: ‘coords’, ‘Error in internal coordinate system’: ‘internal_coords’, ‘FileIO operation on non-existent file.’: ‘missing_file’, ‘FormBX had a problem’: ‘linear_bend’, ‘Inv3 failed in PCMMkU’: ‘solute_solvent_surface’, ‘Linear angle in Tors.’: ‘linear_bend’, ‘No data on chk file.’: ‘empty_file’, ‘Optimization stopped’: ‘opt_steps’, ‘Out-of-memory error in routine’: ‘insufficient_mem’, ‘The combination of multiplicity ([0-9]+) and \\s+? ([0-9]+) electrons is impossible.’: ‘charge’, ‘There are no atoms in this input structure !’: ‘missing_mol’, ‘Z-matrix optimization but no Z-matrix variables.’: ‘coord_inputs’}*
 
-### error_patt  *= re.compile(‘Optimization stopped|Convergence failure|FormBX had a problem|Linear angle in Tors.|Inv3 failed in PCMMkU|Error in internal coordinate system|End of file in ZSymb|There are no atoms in this input str)*
+### error_patt   *= re.compile(‘Optimization stopped|Convergence failure|FormBX had a problem|Linear angle in Tors.|Inv3 failed in PCMMkU|Error in internal coordinate system|End of file in ZSymb|There are no atoms in this input str)*
 
-### grid_patt  *= re.compile(‘(-?\\d{5})’)*
+### grid_patt   *= re.compile(‘(-?\\d{5})’)*
 
-### recom_mem_patt  *= re.compile(‘Use %mem=([0-9]+)MW to provide the minimum amount of memory required to complete this step.’)*
+### recom_mem_patt   *= re.compile(‘Use %mem=([0-9]+)MW to provide the minimum amount of memory required to complete this step.’)*
 
 ## *class* custodian.gaussian.handlers.WallTimeErrorHandler(wall_time: int, buffer_time: int, input_file: str, output_file: str, stderr_file: str = ‘stderr.txt’, prefix: str = ‘error’)
 
@@ -110,7 +110,7 @@ Check if the job is nearing the walltime. If so, return True, else False.
 
 Perform the corrections.
 
-### is_monitor\*: bool\*  *= True*
+### is_monitor\*: bool\*   *= True*
 
 This class property indicates whether the error handler is a monitor,
 i.e., a handler that monitors a job as it is running. If a

docs/custodian.jdftx.jobs.md

@@ -8,7 +8,7 @@ nav_exclude: true
 
 This module implements basic kinds of jobs for JDFTx runs.
 
-### *class* custodian.jdftx.jobs.JDFTxJob(jdftx_cmd, input_file='init.in', output_file='jdftx.out', stderr_file='std_err.txt')
+## *class* custodian.jdftx.jobs.JDFTxJob(jdftx_cmd, input_file=’init.in’, output_file=’jdftx.out’, stderr_file=’std_err.txt’)
 
 Bases: `Job`
 
@@ -23,26 +23,26 @@ A basic JDFTx job. Runs whatever is in the working directory.
   * **stderr_file** (*str*) – Name of file to direct standard error to.
     Defaults to “std_err.txt”.
 
-#### postprocess(directory='./') → None
+### postprocess(directory=’./’) → None
 
 No post-processing required.
 
-#### run(directory='./')
+### run(directory=’./’)
 
 Perform the actual JDFTx run.
 
 ## Returns:
 
 > (subprocess.Popen) Used for monitoring.
 
-#### setup(directory='./') → None
+### setup(directory=’./’) → None
 
 No setup required.
 
-#### terminate(directory='./') → None
+### terminate(directory=’./’) → None
 
 Terminate JDFTx.
 
-#### *static* terminate_process(proc, timeout=5)
+### *static* terminate_process(proc, timeout=5)
 
 Terminate a process gracefully, then forcefully if necessary.

docs/custodian.jdftx.md

@@ -9,7 +9,6 @@ nav_exclude: true
 This package implements various JDFTx Jobs and Error Handlers.
 Used Cp2kJob developed by Nick Winner as a template.
 
-
 * [custodian.jdftx.jobs module](custodian.jdftx.jobs.md)
   * [`JDFTxJob`](custodian.jdftx.jobs.md#custodian.jdftx.jobs.JDFTxJob)
     * [`JDFTxJob.postprocess()`](custodian.jdftx.jobs.md#custodian.jdftx.jobs.JDFTxJob.postprocess)

docs/custodian.nwchem.jobs.md

@@ -17,7 +17,7 @@ A basic Nwchem job.
 Initializes a basic NwChem job.
 
 * **Parameters**
-  * **nwchem_cmd** ( *[**str**]*) – Command to run Nwchem as a list of args. For
+  * **nwchem_cmd** (  *[**str**]*) – Command to run Nwchem as a list of args. For
     example, [“nwchem”].
   * **input_file** (*str*) – Input file to run. Defaults to “mol.nw”.
   * **output_file** (*str*) – Name of file to direct standard out to.
@@ -27,7 +27,7 @@ Initializes a basic NwChem job.
     Defaults to True.
   * **gzipped** (*bool*) – Deprecated. Please use the Custodian class’s
     gzipped_output option instead.
-  * **settings_override** ( *[**dict**]*) – An ansible style list of dict to override changes.
+  * **settings_override** (  *[**dict**]*) – An ansible style list of dict to override changes.
     #TODO: Not implemented yet.
 
 ### postprocess()

docs/custodian.utils.md

@@ -14,7 +14,7 @@ Backup files to a tar.gz file. Used, for example, in backing up the
 files of an errored run before performing corrections.
 
 * **Parameters**
-  * **filenames** ( *[**str**]*) – List of files to backup. Supports wildcards, e.g.,
+  * **filenames** (  *[**str**]*) – List of files to backup. Supports wildcards, e.g.,
      *.*.
   * **prefix** (*str*) – prefix to the files. Defaults to error, which means a
     series of error.1.tar.gz, error.2.tar.gz, … will be generated.