Systematically fix typos in code and documentation (#99)

README.md

@@ -208,7 +208,7 @@ Follow the same instructions above. You shouldn't have to install mingw or modif
 
 
 #### Legacy users
-Warning: pyEPR organization was significnatly improved in v0.8-dev (starting 2020; current branch: master \[to be made stable soon\]). If you used a previous version, you will find that all key classes have been renamed. Please, see the tutorials and docs.  In the meantime, if you cannot switch yet, revert to use the stable v0.7.
+Warning: pyEPR organization was significantly improved in v0.8-dev (starting 2020; current branch: master \[to be made stable soon\]). If you used a previous version, you will find that all key classes have been renamed. Please, see the tutorials and docs.  In the meantime, if you cannot switch yet, revert to use the stable v0.7.
 
 
 # HFSS Project Setup for `pyEPR`
@@ -276,7 +276,7 @@ compiler = mingw32
 [build_ext]
 compiler = mingw32
 ```
-Next, let's install qutip. You can choose to use conda intall or pip install, or pull from the git directly  as done here:
+Next, let's install qutip. You can choose to use conda install or pip install, or pull from the git directly  as done here:
 ```sh
 conda install git
 pip install git+https://github.com/qutip/qutip.git

TODO.md

@@ -2,7 +2,7 @@
 * ./pyEPR/ansys.py
   * LINE 46:	 : Replace `win32com` with Linux compatible package.
   * LINE 795:	 : check if variable does not exist and quit if it doesn't?
-  * LINE 1857: : make mesh tis own  class with preperties
+  * LINE 1857: : make mesh tis own  class with properties
   * LINE 1980: : create Wirebond class
   * LINE 2012: : Add option to modify these
   * LINE 2376: : Add a rotated rectangle object.
@@ -14,7 +14,7 @@
 * ./pyEPR/ansys.py
   * LINE 46:	 : Replace `win32com` with Linux compatible package.
   * LINE 795:	 : check if variable does not exist and quit if it doesn't?
-  * LINE 1857: : make mesh tis own  class with preperties
+  * LINE 1857: : make mesh tis own  class with properties
   * LINE 1980: : create Wirebond class
   * LINE 2012: : Add option to modify these
   * LINE 2376: : Add a rotated rectangle object.
@@ -25,25 +25,25 @@
 
 * ./pyEPR/core_distributed_analysis.py
   * LINE 149: 	: turn into base class shared with analysis!
-  * LINE 253: 	: replace this method with the one below, here because osme funcs use it still
+  * LINE 253: 	: replace this method with the one below, here because some funcs use it still
   * LINE 339: 	: maybe sort column and index? # todo: maybe generalize
   * LINE 488: 	: change to integer?
   * LINE 548: 	: These should be common function to the analysis and here!
   * LINE 849: 	: Update make p saved sep. and get Q for diff materials, indep. specify in pinfo
   * LINE 1046:	: maybe load from data_file
   * LINE 1064:	
-  * LINE 1139:	: Move inside of loop to funciton calle self.analyze_variation
+  * LINE 1139:	: Move inside of loop to function calle self.analyze_variation
   * LINE 1247:	: this should really be passed as argument  to the functions rather than a
   * LINE 1340:	: THis need to be changed, wont work in the future with updating result etc.
   * LINE 1513:	: Move to class for reporter ?
 
 * ./pyEPR/core_quantum_analysis.py
   * LINE 130:	: remove all copies of same data
-  * LINE 574:	: superseed by Convert.ZPF_from_EPR
+  * LINE 574:	: supersede by Convert.ZPF_from_EPR
   * LINE 607:	: avoide analyzing a previously analyzed variation
-  * LINE 741:	: actually make into dataframe with mode labela and junction labels
+  * LINE 741:	: actually make into dataframe with mode labels and junction labels
   * LINE 782:	: ?
-  * LINE 825:	: shouldmove these kwargs to the config
+  * LINE 825:	: should move these kwargs to the config
 
 * ./pyEPR/project_info.py
   * LINE 134:	: introduce modal labels

docs/README.md

@@ -44,7 +44,7 @@ Notes for developers.
   sphinx-apidoc -f -o source/ ../pyEPR -o source/api --no-toc -M -e
   make html
 ```
-You can alos use this to update the doc tree.
+You can also use this to update the doc tree.
 
 # Updating `readthedocs.org`
 

docs/source/index.rst

@@ -21,7 +21,7 @@ Powerful, automated analysis and design of quantum microwave devices
 easy-to-use analysis functions and automation for the design of quantum chips based on superconducting quantum  circuits, both distributed and lumped.
 pyEPR interfaces the classical distributed microwave analysis with that of quantum structures and Hamiltonians.
 It is chiefly based on the `energy participation ratio <https://arxiv.org/abs/1902.10355>`_ approach; however, it has since v0.4 extended to cover a broad range of
-design approaches. pyEPR stradels the analysis from Maxwell's to Schrodinger's equations, and converts the solutions of distributed microwve (typically eignmode simulations)
+design approaches. pyEPR stradels the analysis from Maxwell's to Schrodinger's equations, and converts the solutions of distributed microwave (typically eigenmode simulations)
 to a fully diagonalized spectrum of the energy levels, couplings, and key parameters of a many-body quantum Hamiltonian.
 
 pyEPR contains both analytic and numeric solutions.

docs/source/installation.rst

@@ -42,7 +42,7 @@ Installing locally via pip
 In the future, ``pyEPR`` can be installed using the Python package manager `pip <http://www.pip-installer.org/>`_.
 
 
-However, for the moment, we recommend a local develper instalation, which allows for fast upgrades. We are still in active development.
+However, for the moment, we recommend a local developer installation, which allows for fast upgrades. We are still in active development.
 Perform the steps in the :ref:`install-main` section.
 What you could do, once you have the local clone git, is to install pyEPR locally. Navigate to the local root folder of the repo.
 

docs/source/key_classes_reference.rst

@@ -1,12 +1,12 @@
 Main classes
 =================================
 
-The first main class of pyEPR is :ref:`project-info`, which instansiates and stores the Ansys interfaces classes and user-defined parameters related to the design, such as junction names and properties.
+The first main class of pyEPR is :ref:`project-info`, which instantiates and stores the Ansys interfaces classes and user-defined parameters related to the design, such as junction names and properties.
 
-The second main class of pyEPR is :ref:`distributed-analysis`, which performs the EPR analysis on the ansys eigenfield solutions from the fields. It saves the calculated energy participation ratios (EPRs) and realted convergences, and other paramete results. It does not calculate the Hamiltonian.
+The second main class of pyEPR is :ref:`distributed-analysis`, which performs the EPR analysis on the ansys eigenfield solutions from the fields. It saves the calculated energy participation ratios (EPRs) and related convergences, and other paramete results. It does not calculate the Hamiltonian.
 This is left for the third class.
 
-The third main class of pyEPR is :ref:`quantum-analysis`, which uses the EPRs and other save quantities to create and diagonalizae the Hamiltonian.
+The third main class of pyEPR is :ref:`quantum-analysis`, which uses the EPRs and other save quantities to create and diagonalize the Hamiltonian.
 
 .. _project-info:
 

pyEPR/README.md

@@ -12,8 +12,8 @@ A user should not edit `_config_default.py` directly. A user should overwrite va
 Contains the core analysis and run functions.
 
 ##### toolbox
-Module  that contains key and utility modues used in pyEPR.
-- plotting: useful in visualizaiton and analysis.
+Module  that contains key and utility modules used in pyEPR.
+- plotting: useful in visualization and analysis.
 - pythonic:  useful pythonic functions
 - report: used to plot reports
 
@@ -30,7 +30,7 @@ Contributed by Phil Rheinhold. Originally part of [pyHFSS](https://github.com/Ph
 Updated and modified by Zlatko Minev & Zaki Leghtas.
 
 ##### numeic_diag.py
-Internal use only. For numerical diagonalizaiton.
+Internal use only. For numerical diagonalization.
 Written by Phil Rheinhold.
 Updated by Zlatko Minev & Lysander Christakis.
 This file is tricky, use caution to modify.

pyEPR/__config_user_old.py

@@ -36,7 +36,7 @@
         th=3e-9,
 
         # Surface dielectric (dirt) constant
-        # units: relative permitivity
+        # units: relative permittivity
         eps_r=10,
 
         # Surface dielectric (dirt) loss tangent
@@ -58,7 +58,7 @@
 
     ansys=Dict(
         # method_calc_P_mj sets the method used to calculate the participation ratio in eigenmode.
-        # Valud values:
+        # Valid values:
         # 	'line_voltage' : Uses the line voltage integral
         # 	'J_surf_mag'   : takes the avg. Jsurf over the rect. Make sure you have seeded
         # 					lots of tets here. I recommend starting with 4 across smallest dimension.
@@ -71,7 +71,7 @@
     ),
 
     plotting=Dict(
-        # Default color map for plottng. Better if made into a string name
+        # Default color map for plotting. Better if made into a string name
         # taken from matplotlib.cm
         default_color_map='viridis',  # pylint: disable=no-member
     ),

pyEPR/__init__.py

@@ -147,7 +147,7 @@
         logger.warning(
             """IMPORT WARNING:
         Python package 'pythoncom' could not be loaded
-        It is used in communicting with HFSS on PCs. If you wish to do this, please set it up.
+        It is used in communicating with HFSS on PCs. If you wish to do this, please set it up.
         For Linux, check the HFSS python linux files for the com module used. It is equivalent,
         and can be used just as well.
         %s""", config.internal.error_msg_missing_import)
@@ -168,7 +168,7 @@
     except (ImportError, ModuleNotFoundError):
         logger.error(
             """IMPORT ERROR:
-        Python package 'pint' could not be loaded. It is used in communicting with HFSS. Try:
+        Python package 'pint' could not be loaded. It is used in communicating with HFSS. Try:
             $ conda install -c conda-forge pint \n%s""",
             config.internal.error_msg_missing_import)
 
@@ -185,7 +185,7 @@
 
 from .ansys import parse_units, parse_units_user, parse_entry
 from .core import ProjectInfo, DistributedAnalysis, QuantumAnalysis,\
-                  Project_Info, pyEPR_HFSSAnalysis, pyEPR_Analysis # names to be depricated
+                  Project_Info, pyEPR_HFSSAnalysis, pyEPR_Analysis # names to be deprecated
 
 __all__ = [
     'logger',
@@ -199,7 +199,7 @@
     'QuantumAnalysis',
     'Project_Info',
     'pyEPR_HFSSAnalysis',
-    'pyEPR_Analysis',  # names to be depricated
+    'pyEPR_Analysis',  # names to be deprecated
     'parse_units',
     'parse_units_user',
     'parse_entry'

pyEPR/_config_default.py

@@ -26,7 +26,7 @@
 
     ansys=Dict(
         # method_calc_P_mj sets the method used to calculate the participation ratio in eigenmode.
-        # Valud values:
+        # Valid values:
         # 	'line_voltage' : Uses the line voltage integral
         # 	'J_surf_mag'   : takes the avg. Jsurf over the rect. Make sure you have seeded
         # 					lots of tets here. I recommend starting with 4 across smallest dimension.
@@ -42,14 +42,14 @@
 
     epr = Dict(
 
-        # Define the participation renomalizaiton method
+        # Define the participation renormalization method
         # False : no extra renormalization to enforce
         #         can be more problematic for large pj, when sim isn't well converged
         # True or 1 : use enforcement of U_J_total to be U_mode-U_H
         #         can be more problematic for small pj, when sim isn't well converged
         # 2     : use enforcement of U_J_total to be U_mode-U_H (i.e., 1)
-        #         only when the total particiaption is above a certain threshold
-        #         preffered method.
+        #         only when the total participation is above a certain threshold
+        #         preferred method.
         renorm_pj = 2,
     ),
 
@@ -72,7 +72,7 @@
         th=3e-9,
 
         # Surface dielectric (dirt) constant
-        # units: relative permitivity
+        # units: relative permittivity
         eps_r=10,
 
         # Surface dielectric (dirt) loss tangent
@@ -93,7 +93,7 @@
     ),
 
     plotting=Dict(
-        # Default color map for plottng. Better if made into a string name
+        # Default color map for plotting. Better if made into a string name
         # taken from matplotlib.cm
         default_color_map='viridis',  # pylint: disable=no-member
     ),
@@ -147,7 +147,7 @@ def update_recursive(d:collections.abc.Mapping, u:collections.abc.Mapping):
 
     Arguments:
         d {collections.abc.Mapping} -- dict to overwrite
-        u {collections.abc.Mapping} -- dcit used to update
+        u {collections.abc.Mapping} -- dict used to update
 
     Returns:
         same as d; Updated d
@@ -162,11 +162,11 @@ def update_recursive(d:collections.abc.Mapping, u:collections.abc.Mapping):
 def get_config():
     """Returns the config pointer.
 
-    If the config is not yet loaded, it will load the defualt config and then
+    If the config is not yet loaded, it will load the default config and then
     update it with the _config_user.config dictionary.
 
     Else, it will just return the pointer to the above-updated config, which the
-    user could have modified. The modificaitons will be kept.
+    user could have modified. The modifications will be kept.
 
     Returns:
         Dict : the config dictionary

pyEPR/_config_user.py

@@ -42,7 +42,7 @@
         th=3e-9,
 
         # Surface dielectric (dirt) constant
-        # units: relative permitivity
+        # units: relative permittivity
         eps_r=10,
 
         # Surface dielectric (dirt) loss tangent
@@ -64,7 +64,7 @@
 
     ansys=Dict(
         # method_calc_P_mj sets the method used to calculate the participation ratio in eigenmode.
-        # Valud values:
+        # Valid values:
         # 	'line_voltage' : Uses the line voltage integral
         # 	'J_surf_mag'   : takes the avg. Jsurf over the rect. Make sure you have seeded
         # 					lots of tets here. I recommend starting with 4 across smallest dimension.
@@ -77,7 +77,7 @@
     ),
 
     plotting=Dict(
-        # Default color map for plottng. Better if made into a string name
+        # Default color map for plotting. Better if made into a string name
         # taken from matplotlib.cm
         default_color_map='viridis',  # pylint: disable=no-member
     ),