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Chapter 6 production polish #86

Merged
merged 49 commits into from
Jan 18, 2023
Merged

Chapter 6 production polish #86

merged 49 commits into from
Jan 18, 2023

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trevorcampbell
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@trevorcampbell trevorcampbell commented Jan 2, 2023 •
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@trevorcampbell trevorcampbell marked this pull request as draft January 6, 2023 04:57
@trevorcampbell trevorcampbell marked this pull request as ready for review January 9, 2023 07:25
@trevorcampbell trevorcampbell changed the title [WIP] Chapter 6 production polish Chapter 6 production polish Jan 9, 2023
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@joelostblom there is one figure at the end (Figure 6.7) that is not generating properly --- see the R version to see what the plot should look like). Your help there would be much appreciated.

Aside from that @joelostblom and @lheagy this is ready for review.

Please review the Ch5 PR first #78 since this builds on that one.

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Looking good overall! My biggest comment is the one I made in the issues regarding randomness.

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trevorcampbell and others added 13 commits January 18, 2023 10:49
@trevorcampbell @joelostblom
Update source/classification2.md
26155a0 
Co-authored-by: Joel Ostblom <[email protected]>
@trevorcampbell @joelostblom
Update source/classification2.md
71d52b5 
Co-authored-by: Joel Ostblom <[email protected]>
@trevorcampbell @joelostblom
Update source/classification2.md
36e725f 
Co-authored-by: Joel Ostblom <[email protected]>
@trevorcampbell @joelostblom
Update source/classification2.md
0b7ecc4 
Co-authored-by: Joel Ostblom <[email protected]>
@trevorcampbell @joelostblom
Update source/classification2.md
96493e4 
Co-authored-by: Joel Ostblom <[email protected]>
@trevorcampbell @joelostblom
Update source/classification2.md
1bc8c36 
Co-authored-by: Joel Ostblom <[email protected]>
@trevorcampbell @joelostblom
Update source/classification2.md
d533ac2 
Co-authored-by: Joel Ostblom <[email protected]>
@trevorcampbell @joelostblom
Update source/classification2.md
28ceac8 
Co-authored-by: Joel Ostblom <[email protected]>
@trevorcampbell @joelostblom
Update source/classification2.md
2ef3707 
Co-authored-by: Joel Ostblom <[email protected]>
@trevorcampbell
values -> to_numpy in randomness section
bae52da
@trevorcampbell @joelostblom
Update source/classification2.md
66cf370 
Co-authored-by: Joel Ostblom <[email protected]>
@trevorcampbell @joelostblom
Update source/classification2.md
4a88ec3 
Co-authored-by: Joel Ostblom <[email protected]>
@trevorcampbell
remove code for area plot at the end of ch6
a1f9454
@trevorcampbell trevorcampbell merged commit b6a0f4b into main Jan 18, 2023
trevorcampbell added a commit that referenced this pull request Jan 18, 2023
@trevorcampbell @lheagy
@joelostblom @actions-user
Chapters 5-8 production merge (#139)
4947023 
* welcome (#74)

* update the welcome page to indicate this is the python version, include links to the R version

* minor edits (newline for better diffs)

Co-authored-by: Trevor Campbell <[email protected]>

* put headings on the table of contents for easier navigation (#75)

* Update metadata and add chapter numbering (#44)

* Update _config.yml

* Update repo and branch info

* Make some visible changes

* Include packages we actually use and updated jupyterbook to fix netlify

* Test rebuilding notebooks again

* Fix typo

* Update ToC

* Add ibis

* Always execute all notebooks

* Delete requirements.txt

* Update source/_config.yml

* Update source/_config.yml

* Change path and branch

* Increase timeout

* Update _config.yml (#90)

* Ch3: wrangling (#76)

* wip on ch3

* working on wrangling chapter

* move chaining content to the intro

* update content on summary statistics

* update the disucssion on apply

* remove the discussion on What is a List

* move the assign content to the very end

* minor wordsmithing on welcome page

* edited learning objs in ch1 for new chaining

* update discussion on chaining, edits from Trevor

* update discussion of split

* remove unnecessary call to File: dir	Node: Top	This is the top of the INFO tree
  This (the Directory node) gives a menu of major topics.
  Typing "d" returns here, "q" exits, "?" lists all INFO commands, "h"
  gives a primer for first-timers, "mEmacs<Return>" visits the Emacs topic,
  etc.
  In Emacs, you can click mouse button 2 on a menu item or cross reference
  to select it.
  --- PLEASE ADD DOCUMENTATION TO THIS TREE. (See INFO topic first.) ---

* Menu: The list of major topics begins on the next line.

Emacs
* Ada mode: (ada-mode). The GNU Emacs mode for editing Ada.
* Autotype: (autotype). Convenient features for text that you enter frequently
                          in Emacs.
* CC Mode: (ccmode).   Emacs mode for editing C, C++, Objective-C,
                          Java, Pike, and IDL code.
* CL: (cl).		Partial Common Lisp support for Emacs Lisp.
* Dired-X: (dired-x).   Dired Extra Features.
* EUDC: (eudc).   A client for directory servers (LDAP, PH)
* Ebrowse: (ebrowse).   A C++ class browser for Emacs.
* Ediff: (ediff).       A visual interface for comparing and merging programs.
* Emacs: (emacs).	The extensible self-documenting text editor.
* Emacs FAQ: (efaq).	Frequently Asked Questions about Emacs.
* Emacs MIME: (emacs-mime).   The MIME de/composition library.
* Eshell: (eshell).     A command shell implemented in Emacs Lisp.
* Forms: (forms).	Emacs package for editing data bases
			  by filling in forms.
* Gnus: (gnus).         The newsreader Gnus.
* IDLWAVE: (idlwave).	Major mode and shell for IDL and WAVE/CL files.

* MH-E: (mh-e).		Emacs interface to the MH mail system.
* Message: (message).   Mail and news composition mode that goes with Gnus.
* PCL-CVS: (pcl-cvs).	Emacs front-end to CVS.
* RefTeX: (reftex).	Emacs support for LaTeX cross-references and citations.
* SC: (sc).		Supercite lets you cite parts of messages you're
			  replying to, in flexible ways.

* Speedbar: (speedbar).        File/Tag summarizing utility.
* VIP: (vip).		An older VI-emulation for Emacs.
* VIPER: (viper).       The newest Emacs VI-emulation mode.
                          (also, A VI Plan for Emacs Rescue
                           or the VI PERil.)
* Widget: (widget).      Documenting the "widget" package used by the
                           Emacs Custom facility.
* WoMan: (woman).       Browse UN*X Manual Pages `Wo (without) Man'.

Texinfo documentation system
* Info: (info).                 Documentation browsing system.

Miscellaneous
* Screen: (screen).             Full-screen window manager.
* Standards: (standards).        GNU coding standards.

GNU admin
* Autoconf: (autoconf).         Create source code configuration scripts

Individual utilities
* aclocal: (automake)Invoking aclocal.          Generating aclocal.m4
* autoconf: (autoconf)autoconf Invocation.
                                How to create configuration scripts
* autoreconf: (autoconf)autoreconf Invocation.
                                Remaking multiple `configure' scripts
* autoscan: (autoconf)autoscan Invocation.
                                Semi-automatic `configure.ac' writing
* config.status: (autoconf)config.status Invocation.
                                Recreating a configuration
* configure: (autoconf)configure Invocation.
                                Configuring a package
* ifnames: (autoconf)ifnames Invocation.
                                Listing the conditionals in source code

GNU programming tools
* automake: (automake).		Making Makefile.in's

Utilities
* Bash: (bash).                     The GNU Bourne-Again SHell.

GNU Packages
* Tar: (tar).			Making tape (or disk) archives.

Individual utilities
* tar: (tar)tar invocation.                     Invoking GNU `tar'

Software development
* Cpp: (cpp).		       The GNU C preprocessor.
* Cpplib: (cppinternals).      Cpplib internals.
* gcc: (gcc).                  The GNU Compiler Collection.
* gccinstall: (gccinstall).    Installing the GNU Compiler Collection.
* gccint: (gccint).            Internals of the GNU Compiler Collection.
* gfortran: (gfortran).                  The GNU Fortran Compiler.

GNU Libraries
* libgomp: (libgomp).                    GNU OpenMP runtime library

Programming & development tools
* gdbm_dump: gdbm_dump(gdbm).   Dump the GDBM database into a flat file.
* gdbm_load: gdbm_load(gdbm).   Load the database from a flat file.

Utilities

GNU libraries
* gmp: (gmp).                   GNU Multiple Precision Arithmetic Library.

Software libraries
* GnuTLS: (gnutls).		GNU Transport Layer Security Library.
* GnuTLS-Guile: (gnutls-guile).		GNU Transport Layer Security Library. Guile bindings.
* libidn2: (libidn2).	Internationalized domain names (IDNA2008/TR46) processing.
* libtasn1: (libtasn1). Library for Abstract Syntax Notation One (ASN.1).
* mpfr: (mpfr).                 Multiple Precision Floating-Point Reliable Library.

GNU Packages
* mpc: (mpc)Multiple Precision Complex Library.

Development
* fftw3: (fftw3).	FFTW User's Manual.

Individual utilities
* aclocal-invocation: (automake)aclocal Invocation.   Generating aclocal.m4.
* autoconf-invocation: (autoconf)autoconf Invocation.
                                How to create configuration scripts
* autoheader: (autoconf)autoheader Invocation.
                                How to create configuration templates
* autom4te: (autoconf)autom4te Invocation.
                                The Autoconf executables backbone
* automake-invocation: (automake)automake Invocation. Generating Makefile.in.
* autoreconf: (autoconf)autoreconf Invocation.
                                Remaking multiple ‘configure’ scripts
* autoscan: (autoconf)autoscan Invocation.
                                Semi-automatic ‘configure.ac’ writing
* autoupdate: (autoconf)autoupdate Invocation.
                                Automatic update of ‘configure.ac’
* config.status: (autoconf)config.status Invocation. Recreating configurations.
* configure: (autoconf)configure Invocation.    Configuring a package.
* ifnames: (autoconf)ifnames Invocation.        Listing conditionals in source.
* libtool-invocation: (libtool)Invoking libtool. Running the 'libtool' script.
* libtoolize: (libtool)Invoking libtoolize.      Adding libtool support.
* testsuite: (autoconf)testsuite Invocation.    Running an Autotest test suite.

Software development
* Autoconf: (autoconf).         Create source code configuration scripts.
* Automake: (automake).         Making GNU standards-compliant Makefiles.
* Automake-history: (automake-history). History of Automake development.
* GNU libtextstyle: (libtextstyle).     Output of styled text.
* GNU libunistring: (libunistring).     Unicode string library.
* Libtool: (libtool).           Generic shared library support script.

Localization
* idn2: (libidn2)Invoking idn2.	Internationalized Domain Name (IDNA2008/TR46) conversion.

Encryption
* Nettle: (nettle).             A low-level cryptographic library.

System Administration
* certtool: (gnutls)certtool Invocation.	Manipulate certificates and keys.
* gnutls-cli: (gnutls)gnutls-cli Invocation.	GnuTLS test client.
* gnutls-cli-debug: (gnutls)gnutls-cli-debug Invocation.	GnuTLS debug client.
* gnutls-serv: (gnutls)gnutls-serv Invocation.	GnuTLS test server.
* psktool: (gnutls)psktool Invocation.	Simple TLS-Pre-Shared-Keys manager.
* srptool: (gnutls)srptool Invocation.	Simple SRP password tool.

Libraries
* libgpg-error: (gnupg).   Error codes and common code for GnuPG.

GNU Libraries
* libgcrypt: (gcrypt).  Cryptographic function library.

C++ libraries
* autosprintf: (autosprintf).   Support for printf format strings in C++.

GNU Gettext Utilities
* ISO3166: (gettext)Country Codes.             ISO 3166 country codes.
* ISO639: (gettext)Language Codes.             ISO 639 language codes.
* autopoint: (gettext)autopoint Invocation.    Copy gettext infrastructure.
* envsubst: (gettext)envsubst Invocation.      Expand environment variables.
* gettext: (gettext).                          GNU gettext utilities.
* gettextize: (gettext)gettextize Invocation.  Prepare a package for gettext.
* msgattrib: (gettext)msgattrib Invocation.    Select part of a PO file.
* msgcat: (gettext)msgcat Invocation.          Combine several PO files.
* msgcmp: (gettext)msgcmp Invocation.          Compare a PO file and template.
* msgcomm: (gettext)msgcomm Invocation.        Match two PO files.
* msgconv: (gettext)msgconv Invocation.        Convert PO file to encoding.
* msgen: (gettext)msgen Invocation.            Create an English PO file.
* msgexec: (gettext)msgexec Invocation.        Process a PO file.
* msgfilter: (gettext)msgfilter Invocation.    Pipe a PO file through a filter.
* msgfmt: (gettext)msgfmt Invocation.          Make MO files out of PO files.
* msggrep: (gettext)msggrep Invocation.        Select part of a PO file.
* msginit: (gettext)msginit Invocation.        Create a fresh PO file.
* msgmerge: (gettext)msgmerge Invocation.      Update a PO file from template.
* msgunfmt: (gettext)msgunfmt Invocation.      Uncompile MO file into PO file.
* msguniq: (gettext)msguniq Invocation.        Unify duplicates for PO file.
* ngettext: (gettext)ngettext Invocation.      Translate a message with plural.
* xgettext: (gettext)xgettext Invocation.      Extract strings into a PO file.

The Algorithmic Language Scheme
* Guile Reference: (guile).     The Guile reference manual.
* R5RS: (r5rs).                 The Revised(5) Report on Scheme.

* take care of colons preceding code blocks

* take care of chapter references

* add discussion of lists and dicts

* add table and discussion on basic data structures in python:

* add description of info

* some general cleanup in apply, assign

* typo fix in the intro

* a couple of type fixes:

* polish chaining/multiline exps

* polish ch3 up to and incl tidy data

* polish indexing

* more polish ch3

* fix python exercises link

* more on groupby

* improve groupy and discussion of lambda functions

* try re-ordering the assign and apply content

* global find replace to remove . in naming conventions

* caption on fig24 fixed

* polish up to apply

* cleanup through Using  to create new columns

* through the summery

* add :tags: [output_scroll] for large code outputs, change figure types

* trim vertical whitespace on figures:

* Update source/wrangling.md

Co-authored-by: Joel Ostblom <[email protected]>

* Apply suggestions from code review

Co-authored-by: Joel Ostblom <[email protected]>

* polishing ch3

* final polish on wrangling

* final polish on ch3 joel comments

Co-authored-by: Trevor Campbell <[email protected]>
Co-authored-by: Joel Ostblom <[email protected]>

* added altair_saver extension

* update build_html.sh script with new docker image

* Ch4: Viz (#77)

* code formatting for viz

* update viz chapter

* updating the viz chapter

* comments addressed through faithful dataset

* more progress on the viz chapter (part way through morley data)

* add back code to create the csv for mauna_loa

* a couple minor typo fixes

* polishing ch4

* minor polish on ch4

* code tags in learning objs

* polish on ch4, fixed number -> percentage in figure labels

* re-added other filetypes...

* better line formatting in saving section

* ignore altair warnings; committed faithful plots

* moved faithful plots to img/

* done polishing ch4

Co-authored-by: Trevor Campbell <[email protected]>

* removed unused material

* Front matter (#96)

* preface python

* remove foreword

* added editors page

* fix appendix,references

* added py acks

* minor ed

* Update editors.md

add Lindsey bio

* Add joels bio

Co-authored-by: Lindsey Heagy <[email protected]>
Co-authored-by: Joel Ostblom <[email protected]>

* Add jupyterlab help section (#101)

* Ch1 fig cleanup (#99)

* first figures in ch1:

* code figures for ch1, including ppt to edit them

* update figure sizes

* remove old lingering image

* removed hidden pptx cache file

Co-authored-by: Trevor Campbell <[email protected]>

* Ch2 fig cleanup (#102)

* update output scrolling for ch2

* update scrolling of large output tables

* Ch3 fig cleanup (#103)

* figure polishing for ch3

* more ch3 figures

* Jupyter and Version Control (#98)

* added jupyter and version control back in

* converted bookdown to jupyterbook images in jupyter chapter

* jupyterbook index entries in jupyter

* fig references to jupyterbook in jupytermd

* updated unicode characters in jupyter; added a caveat at the beginning regarding images

* initial index and figure template add to version control

* R -> Python in version control

* fixed figure refs bookdown->jupyterbook in vsn ctl

* jupyterbook index style vsn ctl

* fixed images in vsn ctl

* minor polish

* added caveat

* Update source/version-control.md

* admonitions for caveats

Co-authored-by: Lindsey Heagy <[email protected]>

* remove the visible call of `glue` in the saving section (#109)

* remove the visible call of  in the saving section

* remove size calculation code

* trim whitespace from end of line for better diffs (#111)

* Chapter 5 production polish (#78)

* starting work on ch5+6; categorical type change; remove commented out R code

* value counts, class name remap, replace in ch5

* remove warnings

* polished ch5+6 up to euclidean dist

* minor bugfix

* minor bugfix

* fixed worksheets link at end of chp

* fix minor section heading wording in Ch1

* added nsmallest + note; better chaining for dist comps; removed comments; fixed colors (not working yet)

* initial fit and predict polished; model spec -> model object

* polishing preprocessing

* balancing polished

* pipelines

* learning objs

* mute warnings in ch5

* restore cls2 to main branch

* Update classification1.md

add output scroll for large table

* Update source/classification1.md

Co-authored-by: Joel Ostblom <[email protected]>

* Update source/classification1.md

Co-authored-by: Joel Ostblom <[email protected]>

* Update source/classification1.md

Co-authored-by: Joel Ostblom <[email protected]>

* remove random state specificaiton from ch5

* fixed fill plots

* Update source/classification1.md

Co-authored-by: Joel Ostblom <[email protected]>

* Update source/classification1.md

Co-authored-by: Joel Ostblom <[email protected]>

* Update source/classification1.md

Co-authored-by: Joel Ostblom <[email protected]>

* Update source/classification1.md

Co-authored-by: Joel Ostblom <[email protected]>

* Update source/classification1.md

Co-authored-by: Joel Ostblom <[email protected]>

* better intro of meshgrid

* better warning filtering in chapters 4 and 5

* Update source/classification1.md

Co-authored-by: Joel Ostblom <[email protected]>

* Update source/classification1.md

Co-authored-by: Joel Ostblom <[email protected]>

* Update source/classification1.md

Co-authored-by: Joel Ostblom <[email protected]>

* Update source/classification1.md

Co-authored-by: Joel Ostblom <[email protected]>

* remove np.number and replace with just 'number' in dtype selection

* Update source/classification1.md

Co-authored-by: Joel Ostblom <[email protected]>

* Update source/classification1.md

Co-authored-by: Joel Ostblom <[email protected]>

* properly gluing column names

Co-authored-by: Lindsey Heagy <[email protected]>
Co-authored-by: Joel Ostblom <[email protected]>

* minor fixes post-merge

* Update viz.md (#137)

* Chapter 6 production polish (#86)

* starting work on ch5+6; categorical type change; remove commented out R code

* value counts, class name remap, replace in ch5

* remove warnings

* polished ch5+6 up to euclidean dist

* minor bugfix

* minor bugfix

* fixed worksheets link at end of chp

* fix minor section heading wording in Ch1

* added nsmallest + note; better chaining for dist comps; removed comments; fixed colors (not working yet)

* initial fit and predict polished; model spec -> model object

* polishing preprocessing

* balancing polished

* pipelines

* learning objs

* mute warnings in ch5

* warn mute code; fixed links at end

* restore cls2 to main branch

* remove caption hack; minor fix to learning objs

* Remove caption hack

* initial improved seed explanation

* random seed section polish done

* polished ch6 up to tuning

* initial cross val example done

* in python -> in scikit

* working on cross-val

* polished ch6 up to predictor selection

* commented out predictor selection

* done ch6 except final under/overfit plot

* warnings filter in ch6; remove seed hack cell

* remove reference to random state in train/test split

* minor typesetting .method() vs method

* put setup.md back in to fix broken links

* Update source/classification2.md

Co-authored-by: Joel Ostblom <[email protected]>

* Update source/classification2.md

Co-authored-by: Joel Ostblom <[email protected]>

* Update source/classification2.md

Co-authored-by: Joel Ostblom <[email protected]>

* Update source/classification2.md

Co-authored-by: Joel Ostblom <[email protected]>

* Update source/classification2.md

Co-authored-by: Joel Ostblom <[email protected]>

* Update source/classification2.md

Co-authored-by: Joel Ostblom <[email protected]>

* Update source/classification2.md

Co-authored-by: Joel Ostblom <[email protected]>

* Update source/classification2.md

Co-authored-by: Joel Ostblom <[email protected]>

* Update source/classification2.md

Co-authored-by: Joel Ostblom <[email protected]>

* values -> to_numpy in randomness section

* Update source/classification2.md

Co-authored-by: Joel Ostblom <[email protected]>

* Update source/classification2.md

Co-authored-by: Joel Ostblom <[email protected]>

* remove code for area plot at the end of ch6

Co-authored-by: Joel Ostblom <[email protected]>

* Chapter 7 production polish (#125)

* fix exercises link

* wip

* polished ch7 up to under/overfitting

* done polishing ch7

* Update source/regression1.md

Co-authored-by: Lindsey Heagy <[email protected]>

* Update source/regression1.md

Co-authored-by: Lindsey Heagy <[email protected]>

* Update source/regression1.md

Co-authored-by: Lindsey Heagy <[email protected]>

* Update source/regression1.md

Co-authored-by: Lindsey Heagy <[email protected]>

* Update source/regression1.md

Co-authored-by: Lindsey Heagy <[email protected]>

* Update source/regression1.md

Co-authored-by: Lindsey Heagy <[email protected]>

Co-authored-by: Lindsey Heagy <[email protected]>

* Chapter 8 production polish (#126)

* fix exercises link

* polishing ch8

* done polishing ch8

* Update source/regression2.md

Co-authored-by: Lindsey Heagy <[email protected]>

* Update source/regression2.md

Co-authored-by: Lindsey Heagy <[email protected]>

* Update source/regression2.md

Co-authored-by: Lindsey Heagy <[email protected]>

Co-authored-by: Lindsey Heagy <[email protected]>

Co-authored-by: Lindsey Heagy <[email protected]>
Co-authored-by: Joel Ostblom <[email protected]>
Co-authored-by: GitHub Action <[email protected]>
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Suggestions for Ch6 - Classification 2 classification2
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@trevorcampbell @joelostblom