Computational Methods Course at UdeA. Forked and size reduced from:

Overview

Computational Methods for Physics & Astronomy

Book version at:

https://restrepo.github.io/ComputationalMethods

by: Sebastian Bustamante 2014/2015 Diego Restrepo ** 2017/...

This course is intended for students of Astronomy and Physics at the Universidad de Antioquia and will cover some numerical methods commonly used in science and specially in astronomy. These topics will be addressed from a formal context but also keeping a practical and computational approach, illustrating many useful applications in problems of physics and astronomy.

The practical component will be almost entirely developed in Python and slightly less in C (when computational performance is required). However students with knowledge in other programming languages (except privative languages like MatLab, Mathematica) are also aimed to use them.

In this repository it can be found all the related material of the course, including the detailed program, notes and presentations, examples (ipython notebooks) and homeworks. (This repository may be subject to changes continuously as the course advances).

Submodules help

SYLLABUS: detailed description of the program of the course, including a brief motivation and presentation, topics to be covered, evaluation and bibliography.

Contents

1. Python (1 week)

Topics

Activities

  • Activity 01: Solve the problems in the section Exercises.

2. Mathematical Preliminaries (1 week)

Topics

3. One Variable Equations (2 weeks)

Topics

4. Interpolation Techniques (2 weeks)

Topics

5. Numerical Calculus (2 weeks)

Topics

Activities

6. Linear Algebra (2 weeks)

Topics

7. Differential Equations (2 weeks)

Topics

8. Statistics (1 week)

Topics

Comments
  • Bump nokogiri from 1.12.5 to 1.13.4

    Bump nokogiri from 1.12.5 to 1.13.4

    Bumps nokogiri from 1.12.5 to 1.13.4.

    Release notes

    Sourced from nokogiri's releases.

    1.13.4 / 2022-04-11

    Security

    Dependencies

    • [CRuby] Vendored zlib is updated from 1.2.11 to 1.2.12. (See LICENSE-DEPENDENCIES.md for details on which packages redistribute this library.)
    • [JRuby] Vendored Xerces-J (xerces:xercesImpl) is updated from 2.12.0 to 2.12.2.
    • [JRuby] Vendored nekohtml (org.cyberneko.html) is updated from a fork of 1.9.21 to 1.9.22.noko2. This fork is now publicly developed at https://github.com/sparklemotion/nekohtml

    sha256sum:

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    1.13.3 / 2022-02-21

    Fixed

    • [CRuby] Revert a HTML4 parser bug in libxml 2.9.13 (introduced in Nokogiri v1.13.2). The bug causes libxml2's HTML4 parser to fail to recover when encountering a bare < character in some contexts. This version of Nokogiri restores the earlier behavior, which is to recover from the parse error and treat the < as normal character data (which will be serialized as &lt; in a text node). The bug (and the fix) is only relevant when the RECOVER parse option is set, as it is by default. [#2461]

    SHA256 checksums:

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    </tr></table> 
    

    ... (truncated)

    Changelog

    Sourced from nokogiri's changelog.

    1.13.4 / 2022-04-11

    Security

    Dependencies

    • [CRuby] Vendored zlib is updated from 1.2.11 to 1.2.12. (See LICENSE-DEPENDENCIES.md for details on which packages redistribute this library.)
    • [JRuby] Vendored Xerces-J (xerces:xercesImpl) is updated from 2.12.0 to 2.12.2.
    • [JRuby] Vendored nekohtml (org.cyberneko.html) is updated from a fork of 1.9.21 to 1.9.22.noko2. This fork is now publicly developed at https://github.com/sparklemotion/nekohtml

    1.13.3 / 2022-02-21

    Fixed

    • [CRuby] Revert a HTML4 parser bug in libxml 2.9.13 (introduced in Nokogiri v1.13.2). The bug causes libxml2's HTML4 parser to fail to recover when encountering a bare < character in some contexts. This version of Nokogiri restores the earlier behavior, which is to recover from the parse error and treat the < as normal character data (which will be serialized as &lt; in a text node). The bug (and the fix) is only relevant when the RECOVER parse option is set, as it is by default. [#2461]

    1.13.2 / 2022-02-21

    Security

    • [CRuby] Vendored libxml2 is updated from 2.9.12 to 2.9.13. This update addresses CVE-2022-23308.
    • [CRuby] Vendored libxslt is updated from 1.1.34 to 1.1.35. This update addresses CVE-2021-30560.

    Please see GHSA-fq42-c5rg-92c2 for more information about these CVEs.

    Dependencies

    1.13.1 / 2022-01-13

    Fixed

    • Fix Nokogiri::XSLT.quote_params regression in v1.13.0 that raised an exception when non-string stylesheet parameters were passed. Non-string parameters (e.g., integers and symbols) are now explicitly supported and both keys and values will be stringified with #to_s. [#2418]
    • Fix CSS selector query regression in v1.13.0 that raised an Nokogiri::XML::XPath::SyntaxError when parsing XPath attributes mixed into the CSS query. Although this mash-up of XPath and CSS syntax previously worked unintentionally, it is now an officially supported feature and is documented as such. [#2419]

    1.13.0 / 2022-01-06

    ... (truncated)

    Commits
    • 4e2c4b2 version bump to v1.13.4
    • 6a20ee4 Merge pull request #2510 from sparklemotion/flavorjones-encoding-reader-perfo...
    • b848031 Merge pull request #2509 from sparklemotion/flavorjones-parse-processing-inst...
    • c0ecf3b test: pend the LIBXML_LOADED_VERSION test on freebsd
    • e444525 fix(perf): HTML4::EncodingReader detection
    • 1eb5580 style(rubocop): allow intentional use of empty initializer
    • 0feac5a fix(dep): HTML parsing of processing instructions
    • db72b90 test: recent nekohtml versions do not consider 'a' to be inline
    • 2af2a87 style(rubocop): allow intentional use of empty initializer
    • ba7a28c Merge pull request #2499 from sparklemotion/2441-xerces-2.12.2-backport-v1.13.x
    • Additional commits viewable in compare view

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    dependencies 
    opened by dependabot[bot] 1
  • Bump nokogiri from 1.12.5 to 1.13.3

    Bump nokogiri from 1.12.5 to 1.13.3

    Bumps nokogiri from 1.12.5 to 1.13.3.

    Release notes

    Sourced from nokogiri's releases.

    1.13.3 / 2022-02-21

    Fixed

    • [CRuby] Revert a HTML4 parser bug in libxml 2.9.13 (introduced in Nokogiri v1.13.2). The bug causes libxml2's HTML4 parser to fail to recover when encountering a bare < character in some contexts. This version of Nokogiri restores the earlier behavior, which is to recover from the parse error and treat the < as normal character data (which will be serialized as &lt; in a text node). The bug (and the fix) is only relevant when the RECOVER parse option is set, as it is by default. [#2461]

    SHA256 checksums:

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    1.13.2 / 2022-02-21

    Security

    • [CRuby] Vendored libxml2 is updated from 2.9.12 to 2.9.13. This update addresses CVE-2022-23308.
    • [CRuby] Vendored libxslt is updated from 1.1.34 to 1.1.35. This update addresses CVE-2021-30560.

    Please see GHSA-fq42-c5rg-92c2 for more information about these CVEs.

    Dependencies


    SHA256 checksums:

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    </tr></table> 
    

    ... (truncated)

    Changelog

    Sourced from nokogiri's changelog.

    1.13.3 / 2022-02-21

    Fixed

    • [CRuby] Revert a HTML4 parser bug in libxml 2.9.13 (introduced in Nokogiri v1.13.2). The bug causes libxml2's HTML4 parser to fail to recover when encountering a bare < character in some contexts. This version of Nokogiri restores the earlier behavior, which is to recover from the parse error and treat the < as normal character data (which will be serialized as &lt; in a text node). The bug (and the fix) is only relevant when the RECOVER parse option is set, as it is by default. [#2461]

    1.13.2 / 2022-02-21

    Security

    • [CRuby] Vendored libxml2 is updated from 2.9.12 to 2.9.13. This update addresses CVE-2022-23308.
    • [CRuby] Vendored libxslt is updated from 1.1.34 to 1.1.35. This update addresses CVE-2021-30560.

    Please see GHSA-fq42-c5rg-92c2 for more information about these CVEs.

    Dependencies

    1.13.1 / 2022-01-13

    Fixed

    • Fix Nokogiri::XSLT.quote_params regression in v1.13.0 that raised an exception when non-string stylesheet parameters were passed. Non-string parameters (e.g., integers and symbols) are now explicitly supported and both keys and values will be stringified with #to_s. [#2418]
    • Fix CSS selector query regression in v1.13.0 that raised an Nokogiri::XML::XPath::SyntaxError when parsing XPath attributes mixed into the CSS query. Although this mash-up of XPath and CSS syntax previously worked unintentionally, it is now an officially supported feature and is documented as such. [#2419]

    1.13.0 / 2022-01-06

    Notes

    Ruby

    This release introduces native gem support for Ruby 3.1. Please note that Windows users should use the x64-mingw-ucrt platform gem for Ruby 3.1, and x64-mingw32 for Ruby 2.6–3.0 (see RubyInstaller 3.1.0 release notes).

    This release ends support for:

    Faster, more reliable installation: Native Gem for ARM64 Linux

    This version of Nokogiri ships experimental native gem support for the aarch64-linux platform, which should support AWS Graviton and other ARM Linux platforms. We don't yet have CI running for this platform, and so we're interested in hearing back from y'all whether this is working, and what problems you're seeing. Please send us feedback here: Feedback: Have you used the aarch64-linux native gem?

    ... (truncated)

    Commits
    • 7d74ced version bump to v1.13.3
    • 5970fd9 fix: revert libxml2 regression with HTML4 recovery
    • 49b8663 version bump to v1.13.2
    • 4729133 Merge pull request #2457 from sparklemotion/flavorjones-libxml-2.9.13-v1.13.x
    • 379f757 dev(package): work around gnome mirrors with expired certs
    • 95cf66c dep: upgrade libxml2 2.9.12 → 2.9.13
    • d37dd02 dep: upgrade libxslt 1.1.34 → 1.1.35
    • 59a9398 dep: upgrade mini_portile 2.7 to 2.8
    • e885463 dev(package): handle either .tar.gz or .tar.xz archive names
    • 7957c7b style: rubocop
    • Additional commits viewable in compare view

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    dependencies 
    opened by dependabot[bot] 1
  • Bump nokogiri from 1.10.9 to 1.11.5

    Bump nokogiri from 1.10.9 to 1.11.5

    Bumps nokogiri from 1.10.9 to 1.11.5.

    Release notes

    Sourced from nokogiri's releases.

    1.11.5 / 2021-05-19

    Fixed

    [Windows CRuby] Work around segfault at process exit on Windows when using libxml2 system DLLs.

    libxml 2.9.12 introduced new behavior to avoid memory leaks when unloading libxml2 shared libraries (see libxml/!66). Early testing caught this segfault on non-Windows platforms (see #2059 and libxml@956534e) but it was incompletely fixed and is still an issue on Windows platforms that are using system DLLs.

    We work around this by configuring libxml2 in this situation to use its default memory management functions. Note that if Nokogiri is not on Windows, or is not using shared system libraries, it will will continue to configure libxml2 to use Ruby's memory management functions. Nokogiri::VERSION_INFO["libxml"]["memory_management"] will allow you to verify when the default memory management functions are being used. [#2241]

    Added

    Nokogiri::VERSION_INFO["libxml"] now contains the key "memory_management" to declare whether libxml2 is using its default memory management functions, or whether it uses the memory management functions from ruby. See above for more details.

    1.11.4 / 2021-05-14

    Security

    [CRuby] Vendored libxml2 upgraded to v2.9.12 which addresses:

    Note that two additional CVEs were addressed upstream but are not relevant to this release. CVE-2021-3516 via xmllint is not present in Nokogiri, and CVE-2020-7595 has been patched in Nokogiri since v1.10.8 (see #1992).

    Please see nokogiri/GHSA-7rrm-v45f-jp64 or #2233 for a more complete analysis of these CVEs and patches.

    Dependencies

    • [CRuby] vendored libxml2 is updated from 2.9.10 to 2.9.12. (Note that 2.9.11 was skipped because it was superseded by 2.9.12 a few hours after its release.)

    1.11.3 / 2021-04-07

    Fixed

    • [CRuby] Passing non-Node objects to Document#root= now raises an ArgumentError exception. Previously this likely segfaulted. [#1900]
    • [JRuby] Passing non-Node objects to Document#root= now raises an ArgumentError exception. Previously this raised a TypeError exception.
    • [CRuby] arm64/aarch64 systems (like Apple's M1) can now compile libxml2 and libxslt from source (though we continue to strongly advise users to install the native gems for the best possible experience)

    1.11.2 / 2021-03-11

    ... (truncated)

    Changelog

    Sourced from nokogiri's changelog.

    1.11.5 / 2021-05-19

    Fixed

    [Windows CRuby] Work around segfault at process exit on Windows when using libxml2 system DLLs.

    libxml 2.9.12 introduced new behavior to avoid memory leaks when unloading libxml2 shared libraries (see libxml/!66). Early testing caught this segfault on non-Windows platforms (see #2059 and libxml@956534e) but it was incompletely fixed and is still an issue on Windows platforms that are using system DLLs.

    We work around this by configuring libxml2 in this situation to use its default memory management functions. Note that if Nokogiri is not on Windows, or is not using shared system libraries, it will will continue to configure libxml2 to use Ruby's memory management functions. Nokogiri::VERSION_INFO["libxml"]["memory_management"] will allow you to verify when the default memory management functions are being used. [#2241]

    Added

    Nokogiri::VERSION_INFO["libxml"] now contains the key "memory_management" to declare whether libxml2 is using its default memory management functions, or whether it uses the memory management functions from ruby. See above for more details.

    1.11.4 / 2021-05-14

    Security

    [CRuby] Vendored libxml2 upgraded to v2.9.12 which addresses:

    Note that two additional CVEs were addressed upstream but are not relevant to this release. CVE-2021-3516 via xmllint is not present in Nokogiri, and CVE-2020-7595 has been patched in Nokogiri since v1.10.8 (see #1992).

    Please see nokogiri/GHSA-7rrm-v45f-jp64 or #2233 for a more complete analysis of these CVEs and patches.

    Dependencies

    • [CRuby] vendored libxml2 is updated from 2.9.10 to 2.9.12. (Note that 2.9.11 was skipped because it was superseded by 2.9.12 a few hours after its release.)

    1.11.3 / 2021-04-07

    Fixed

    • [CRuby] Passing non-Node objects to Document#root= now raises an ArgumentError exception. Previously this likely segfaulted. [#1900]
    • [JRuby] Passing non-Node objects to Document#root= now raises an ArgumentError exception. Previously this raised a TypeError exception.
    • [CRuby] arm64/aarch64 systems (like Apple's M1) can now compile libxml2 and libxslt from source (though we continue to strongly advise users to install the native gems for the best possible experience)

    1.11.2 / 2021-03-11

    ... (truncated)

    Commits
    • e43f521 version bump to v1.11.5
    • 42354e4 Merge pull request #2243 from sparklemotion/flavorjones-v1_11_x-update-tests-...
    • 05f30eb update CHANGELOG
    • e6709aa windows: work around libxml2 xmlCleanupParser
    • 8f54c0f test: adjust tests to pass on system libxml2 >= 2.9.11
    • 3d8a570 ci: windows config for github actions
    • 4b9bfe3 update CHANGELOG with the GHSA
    • 9d69b44 version bump to v1.11.4
    • 058e87f update CHANGELOG with complete CVE information
    • 9285251 Merge pull request #2234 from sparklemotion/2233-upgrade-to-libxml-2-9-12
    • Additional commits viewable in compare view

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    dependencies 
    opened by dependabot[bot] 1
  • Bump nokogiri from 1.10.9 to 1.11.1

    Bump nokogiri from 1.10.9 to 1.11.1

    Bumps nokogiri from 1.10.9 to 1.11.1.

    Release notes

    Sourced from nokogiri's releases.

    v1.11.1 / 2021-01-06

    Fixed

    • [CRuby] If libxml-ruby is loaded before nokogiri, the SAX and Push parsers no longer call libxml-ruby's handlers. Instead, they defensively override the libxml2 global handler before parsing. [#2168]

    SHA-256 Checksums of published gems

    a41091292992cb99be1b53927e1de4abe5912742ded956b0ba3383ce4f29711c  nokogiri-1.11.1-arm64-darwin.gem
    d44fccb8475394eb71f29dfa7bb3ac32ee50795972c4557ffe54122ce486479d  nokogiri-1.11.1-java.gem
    f760285e3db732ee0d6e06370f89407f656d5181a55329271760e82658b4c3fc  nokogiri-1.11.1-x64-mingw32.gem
    dd48343bc4628936d371ba7256c4f74513b6fa642e553ad7401ce0d9b8d26e1f  nokogiri-1.11.1-x86-linux.gem
    7f49138821d714fe2c5d040dda4af24199ae207960bf6aad4a61483f896bb046  nokogiri-1.11.1-x86-mingw32.gem
    5c26111f7f26831508cc5234e273afd93f43fbbfd0dcae5394490038b88d28e7  nokogiri-1.11.1-x86_64-darwin.gem
    c3617c0680af1dd9fda5c0fd7d72a0da68b422c0c0b4cebcd7c45ff5082ea6d2  nokogiri-1.11.1-x86_64-linux.gem
    42c2a54dd3ef03ef2543177bee3b5308313214e99f0d1aa85f984324329e5caa  nokogiri-1.11.1.gem
    

    v1.11.0 / 2021-01-03

    Notes

    Faster, more reliable installation: Native Gems for Linux and OSX/Darwin

    "Native gems" contain pre-compiled libraries for a specific machine architecture. On supported platforms, this removes the need for compiling the C extension and the packaged libraries. This results in much faster installation and more reliable installation, which as you probably know are the biggest headaches for Nokogiri users.

    We've been shipping native Windows gems since 2009, but starting in v1.11.0 we are also shipping native gems for these platforms:

    • Linux: x86-linux and x86_64-linux -- including musl platforms like alpine
    • OSX/Darwin: x86_64-darwin and arm64-darwin

    We'd appreciate your thoughts and feedback on this work at #2075.

    Dependencies

    Ruby

    This release introduces support for Ruby 2.7 and 3.0 in the precompiled native gems.

    This release ends support for:

    Gems

    ... (truncated)

    Changelog

    Sourced from nokogiri's changelog.

    v1.11.1 / 2021-01-06

    Fixed

    • [CRuby] If libxml-ruby is loaded before nokogiri, the SAX and Push parsers no longer call libxml-ruby's handlers. Instead, they defensively override the libxml2 global handler before parsing. [#2168]

    v1.11.0 / 2021-01-03

    Notes

    Faster, more reliable installation: Native Gems for Linux and OSX/Darwin

    "Native gems" contain pre-compiled libraries for a specific machine architecture. On supported platforms, this removes the need for compiling the C extension and the packaged libraries. This results in much faster installation and more reliable installation, which as you probably know are the biggest headaches for Nokogiri users.

    We've been shipping native Windows gems since 2009, but starting in v1.11.0 we are also shipping native gems for these platforms:

    • Linux: x86-linux and x86_64-linux -- including musl platforms like alpine
    • OSX/Darwin: x86_64-darwin and arm64-darwin

    We'd appreciate your thoughts and feedback on this work at #2075.

    Dependencies

    Ruby

    This release introduces support for Ruby 2.7 and 3.0 in the precompiled native gems.

    This release ends support for:

    Gems

    Security

    See note below about CVE-2020-26247 in the "Changed" subsection entitled "XML::Schema parsing treats input as untrusted by default".

    Added

    • Add Node methods for manipulating "keyword attributes" (for example, class and rel): #kwattr_values, #kwattr_add, #kwattr_append, and #kwattr_remove. [#2000]

    ... (truncated)

    Commits
    • 7be6f04 version bump to v1.11.1
    • aa0c399 dev: overhaul .gitignore
    • 3d90c6d Merge pull request #2169 from sparklemotion/2168-active-support-test-failure
    • bbf850c changelog: update for #2168
    • ee69772 ci: another valgrind suppression
    • f9a2c4e fix: restore proper error handling in the SAX push parser
    • 35aa88b fix(cruby): reset libxml2's error handler in sax and push parsers
    • 07459fd fix(test): clobber libxml2's global error handler before every test
    • b682ac5 ci: ensure all tests are running setup
    • 007662f github: update "installation difficulty" issue template
    • Additional commits viewable in compare view

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    dependencies 
    opened by dependabot[bot] 1
  • Bump nokogiri from 1.10.9 to 1.12.5

    Bump nokogiri from 1.10.9 to 1.12.5

    Bumps nokogiri from 1.10.9 to 1.12.5.

    Release notes

    Sourced from nokogiri's releases.

    1.12.5 / 2021-09-27

    Security

    [JRuby] Address CVE-2021-41098 (GHSA-2rr5-8q37-2w7h).

    In Nokogiri v1.12.4 and earlier, on JRuby only, the SAX parsers resolve external entities (XXE) by default. This fix turns off entity-resolution-by-default in the JRuby SAX parsers to match the CRuby SAX parsers' behavior.

    CRuby users are not affected by this CVE.

    Fixed

    • [CRuby] Document#to_xhtml properly serializes self-closing tags in libxml > 2.9.10. A behavior change introduced in libxml 2.9.11 resulted in emitting start and and tags (e.g., <br></br>) instead of a self-closing tag (e.g., <br/>) in previous Nokogiri versions. [#2324]

    SHA256 checksums:

    36bfa3a07aced069b3f3c9b39d9fb62cb0728d284d02b079404cd55780beaeff  nokogiri-1.12.5-arm64-darwin.gem
    16b1a9ddbb70a9c998462912a5972097cbc79c3e01eb373906886ef8a469f589  nokogiri-1.12.5-java.gem
    218dcc6edd1b49cc6244b5f88afb978739bb2f3f166c271557fe5f51e4bc713c  nokogiri-1.12.5-x64-mingw32.gem
    e33bb919d64c16d931a5f26dc880969e587d225cfa97e6b56e790fb52179f527  nokogiri-1.12.5-x86-linux.gem
    e13c2ed011b8346fbd589e96fe3542d763158bc2c7ad0f4f55f6d801afd1d9ff  nokogiri-1.12.5-x86-mingw32.gem
    1ed64f7db7c1414b87fce28029f2a10128611d2037e0871ba298d00f9a00edd6  nokogiri-1.12.5-x86_64-darwin.gem
    0868c8d0a147904d4dedaaa05af5f06656f2d3c67e4432601718559bf69d6cea  nokogiri-1.12.5-x86_64-linux.gem
    2b20905942acc580697c8c496d0d1672ab617facb9d30d156b3c7676e67902ec  nokogiri-1.12.5.gem
    

    1.12.4 / 2021-08-29

    Notable fix: Namespace inheritance

    Namespace behavior when reparenting nodes has historically been poorly specified and the behavior diverged between CRuby and JRuby. As a result, making this behavior consistent in v1.12.0 introduced a breaking change.

    This patch release reverts the Builder behavior present in v1.12.0..v1.12.3 but keeps the Document behavior. This release also introduces a Document attribute to allow affected users to easily change this behavior for their legacy code without invasive changes.

    Compensating Feature in XML::Document

    This release of Nokogiri introduces a new Document boolean attribute, namespace_inheritance, which controls whether children should inherit a namespace when they are reparented. Nokogiri::XML:Document defaults this attribute to false meaning "do not inherit," thereby making explicit the behavior change introduced in v1.12.0.

    CRuby users who desire the pre-v1.12.0 behavior may set document.namespace_inheritance = true before reparenting nodes.

    See https://nokogiri.org/rdoc/Nokogiri/XML/Document.html#namespace_inheritance-instance_method for example usage.

    Fix for XML::Builder

    ... (truncated)

    Changelog

    Sourced from nokogiri's changelog.

    1.12.5 / 2021-09-27

    Security

    [JRuby] Address CVE-2021-41098 (GHSA-2rr5-8q37-2w7h).

    In Nokogiri v1.12.4 and earlier, on JRuby only, the SAX parsers resolve external entities (XXE) by default. This fix turns off entity-resolution-by-default in the JRuby SAX parsers to match the CRuby SAX parsers' behavior.

    CRuby users are not affected by this CVE.

    Fixed

    • [CRuby] Document#to_xhtml properly serializes self-closing tags in libxml > 2.9.10. A behavior change introduced in libxml 2.9.11 resulted in emitting start and and tags (e.g., <br></br>) instead of a self-closing tag (e.g., <br/>) in previous Nokogiri versions. [#2324]

    1.12.4 / 2021-08-29

    Notable fix: Namespace inheritance

    Namespace behavior when reparenting nodes has historically been poorly specified and the behavior diverged between CRuby and JRuby. As a result, making this behavior consistent in v1.12.0 introduced a breaking change.

    This patch release reverts the Builder behavior present in v1.12.0..v1.12.3 but keeps the Document behavior. This release also introduces a Document attribute to allow affected users to easily change this behavior for their legacy code without invasive changes.

    Compensating Feature in XML::Document

    This release of Nokogiri introduces a new Document boolean attribute, namespace_inheritance, which controls whether children should inherit a namespace when they are reparented. Nokogiri::XML:Document defaults this attribute to false meaning "do not inherit," thereby making explicit the behavior change introduced in v1.12.0.

    CRuby users who desire the pre-v1.12.0 behavior may set document.namespace_inheritance = true before reparenting nodes.

    See https://nokogiri.org/rdoc/Nokogiri/XML/Document.html#namespace_inheritance-instance_method for example usage.

    Fix for XML::Builder

    However, recognizing that we want Builder-created children to inherit namespaces, Builder now will set namespace_inheritance=true on the underlying document for both JRuby and CRuby. This means that, on CRuby, the pre-v1.12.0 behavior is restored.

    Users who want to turn this behavior off may pass a keyword argument to the Builder constructor like so:

    Nokogiri::XML::Builder.new(namespace_inheritance: false)
    

    See https://nokogiri.org/rdoc/Nokogiri/XML/Builder.html#label-Namespace+inheritance for example usage.

    Downstream gem maintainers

    Note that any downstream gems may want to specifically omit Nokogiri v1.12.0--v1.12.3 from their dependency specification if they rely on child namespace inheritance:

    ... (truncated)

    Commits
    • 47f6a46 version bump to v1.12.5
    • 2a0ac88 update CHANGELOG
    • 6b60637 Merge pull request #2329 from sparklemotion/flavorjones-GHSA-2rr5-8q37-2w7h_1...
    • 4bd943c fix(jruby): SAX parser uses an entity resolver
    • f943ee4 refactor(jruby): handle errors more consistently
    • 2790122 format: test files
    • 01e1618 Merge pull request #2327 from sparklemotion/2324-xhtml-self-closing-tags_v1.12.x
    • a0180c7 fix: HTML4::Document.to_xhtml self-closing tags
    • 564ac17 release v1.12.4
    • 4d5754b backport #2320
    • Additional commits viewable in compare view

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    dependencies 
    opened by dependabot[bot] 0
  • Bump addressable from 2.7.0 to 2.8.0

    Bump addressable from 2.7.0 to 2.8.0

    Bumps addressable from 2.7.0 to 2.8.0.

    Changelog

    Sourced from addressable's changelog.

    Addressable 2.8.0

    • fixes ReDoS vulnerability in Addressable::Template#match
    • no longer replaces + with spaces in queries for non-http(s) schemes
    • fixed encoding ipv6 literals
    • the :compacted flag for normalized_query now dedupes parameters
    • fix broken escape_component alias
    • dropping support for Ruby 2.0 and 2.1
    • adding Ruby 3.0 compatibility for development tasks
    • drop support for rack-mount and remove Addressable::Template#generate
    • performance improvements
    • switch CI/CD to GitHub Actions
    Commits
    • 6469a23 Updating gemspec again
    • 2433638 Merge branch 'main' of github.com:sporkmonger/addressable into main
    • e9c76b8 Merge pull request #378 from ashmaroli/flat-map
    • 56c5cf7 Update the gemspec
    • c1fed1c Require a non-vulnerable rake
    • 0d8a312 Adding note about ReDoS vulnerability
    • 89c7613 Merge branch 'template-regexp' into main
    • cf8884f Note about alias fix
    • bb03f71 Merge pull request #371 from charleystran/add_missing_encode_component_doc_entry
    • 6d1d809 Adding note about :compacted normalization
    • Additional commits viewable in compare view

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    dependencies 
    opened by dependabot[bot] 0
  • Bump nokogiri from 1.10.4 to 1.10.9

    Bump nokogiri from 1.10.4 to 1.10.9

    Bumps nokogiri from 1.10.4 to 1.10.9.

    Release notes

    Sourced from nokogiri's releases.

    1.10.9 / 2020-03-01

    Fixed

    • [MRI] Raise an exception when Nokogiri detects a specific libxml2 edge case involving blank Schema nodes wrapped by Ruby objects that would cause a segfault. Currently no fix is available upstream, so we're preventing a dangerous operation and informing users to code around it if possible. [#1985, #2001]
    • [JRuby] Change NodeSet#to_a to return a RubyArray instead of Object, for compilation under JRuby 9.2.9 and later. [#1968, #1969] (Thanks, @headius!)

    1.10.8 / 2020-02-10

    Security

    [MRI] Pulled in upstream patch from libxml that addresses CVE-2020-7595. Full details are available in #1992. Note that this patch is not yet (as of 2020-02-10) in an upstream release of libxml.

    1.10.7 / 2019-12-03

    Bug

    • [MRI] Ensure the patch applied in v1.10.6 works with GNU patch. #1954

    1.10.6 / 2019-12-03

    Bug

    • [MRI] Fix FreeBSD installation of vendored libxml2. [#1941, #1953] (Thanks, @nurse!)

    1.10.5 / 2019-10-31

    Dependencies

    • [MRI] vendored libxml2 is updated from 2.9.9 to 2.9.10
    • [MRI] vendored libxslt is updated from 1.1.33 to 1.1.34
    Changelog

    Sourced from nokogiri's changelog.

    1.10.9 / 2020-03-01

    Fixed

    • [MRI] Raise an exception when Nokogiri detects a specific libxml2 edge case involving blank Schema nodes wrapped by Ruby objects that would cause a segfault. Currently no fix is available upstream, so we're preventing a dangerous operation and informing users to code around it if possible. [#1985, #2001]
    • [JRuby] Change NodeSet#to_a to return a RubyArray instead of Object, for compilation under JRuby 9.2.9 and later. [#1968, #1969] (Thanks, @headius!)

    1.10.8 / 2020-02-10

    Security

    [MRI] Pulled in upstream patch from libxml that addresses CVE-2020-7595. Full details are available in #1992. Note that this patch is not yet (as of 2020-02-10) in an upstream release of libxml.

    1.10.7 / 2019-12-03

    Fixed

    • [MRI] Ensure the patch applied in v1.10.6 works with GNU patch. [#1954]

    1.10.6 / 2019-12-03

    Fixed

    • [MRI] Fix FreeBSD installation of vendored libxml2. [#1941, #1953] (Thanks, @nurse!)

    1.10.5 / 2019-10-31

    Security

    [MRI] Vendored libxslt upgraded to v1.1.34 which addresses three CVEs for libxslt:

    • CVE-2019-13117
    • CVE-2019-13118
    • CVE-2019-18197
    • CVE-2019-19956

    More details are available at #1943.

    Dependencies

    • [MRI] vendored libxml2 is updated from 2.9.9 to 2.9.10
    • [MRI] vendored libxslt is updated from 1.1.33 to 1.1.34
    Commits

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    dependencies 
    opened by dependabot[bot] 0
  • Bump tzinfo from 1.2.5 to 1.2.10

    Bump tzinfo from 1.2.5 to 1.2.10

    Bumps tzinfo from 1.2.5 to 1.2.10.

    Release notes

    Sourced from tzinfo's releases.

    v1.2.10

    TZInfo v1.2.10 on RubyGems.org

    v1.2.9

    • Fixed an incorrect InvalidTimezoneIdentifier exception raised when loading a zoneinfo file that includes rules specifying an additional transition to the final defined offset (for example, Africa/Casablanca in version 2018e of the Time Zone Database). #123.

    TZInfo v1.2.9 on RubyGems.org

    v1.2.8

    • Added support for handling "slim" format zoneinfo files that are produced by default by zic version 2020b and later. The POSIX-style TZ string is now used calculate DST transition times after the final defined transition in the file. The 64-bit section is now always used regardless of whether Time has support for 64-bit times. #120.
    • Rubinius is no longer supported.

    TZInfo v1.2.8 on RubyGems.org

    v1.2.7

    • Fixed 'wrong number of arguments' errors when running on JRuby 9.0. #114.
    • Fixed warnings when running on Ruby 2.8. #112.

    TZInfo v1.2.7 on RubyGems.org

    v1.2.6

    • Timezone#strftime('%s', time) will now return the correct number of seconds since the epoch. #91.
    • Removed the unused TZInfo::RubyDataSource::REQUIRE_PATH constant.
    • Fixed "SecurityError: Insecure operation - require" exceptions when loading data with recent Ruby releases in safe mode.
    • Fixed warnings when running on Ruby 2.7. #106 and #111.

    TZInfo v1.2.6 on RubyGems.org

    Changelog

    Sourced from tzinfo's changelog.

    Version 1.2.10 - 19-Jul-2022

    Version 1.2.9 - 16-Dec-2020

    • Fixed an incorrect InvalidTimezoneIdentifier exception raised when loading a zoneinfo file that includes rules specifying an additional transition to the final defined offset (for example, Africa/Casablanca in version 2018e of the Time Zone Database). #123.

    Version 1.2.8 - 8-Nov-2020

    • Added support for handling "slim" format zoneinfo files that are produced by default by zic version 2020b and later. The POSIX-style TZ string is now used calculate DST transition times after the final defined transition in the file. The 64-bit section is now always used regardless of whether Time has support for 64-bit times. #120.
    • Rubinius is no longer supported.

    Version 1.2.7 - 2-Apr-2020

    • Fixed 'wrong number of arguments' errors when running on JRuby 9.0. #114.
    • Fixed warnings when running on Ruby 2.8. #112.

    Version 1.2.6 - 24-Dec-2019

    • Timezone#strftime('%s', time) will now return the correct number of seconds since the epoch. #91.
    • Removed the unused TZInfo::RubyDataSource::REQUIRE_PATH constant.
    • Fixed "SecurityError: Insecure operation - require" exceptions when loading data with recent Ruby releases in safe mode.
    • Fixed warnings when running on Ruby 2.7. #106 and #111.
    Commits
    • 0814dcd Fix the release date.
    • fd05e2a Preparing v1.2.10.
    • b98c32e Merge branch 'fix-directory-traversal-1.2' into 1.2
    • ac3ee68 Remove unnecessary escaping of + within regex character classes.
    • 9d49bf9 Fix relative path loading tests.
    • 394c381 Remove private_constant for consistency and compatibility.
    • 5e9f990 Exclude Arch Linux's SECURITY file from the time zone index.
    • 17fc9e1 Workaround for 'Permission denied - NUL' errors with JRuby on Windows.
    • 6bd7a51 Update copyright years.
    • 9905ca9 Fix directory traversal in Timezone.get when using Ruby data source
    • Additional commits viewable in compare view

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    dependencies 
    opened by dependabot[bot] 0
  • Bump nokogiri from 1.12.5 to 1.13.6

    Bump nokogiri from 1.12.5 to 1.13.6

    Bumps nokogiri from 1.12.5 to 1.13.6.

    Release notes

    Sourced from nokogiri's releases.

    1.13.6 / 2022-05-08

    Security

    • [CRuby] Address CVE-2022-29181, improper handling of unexpected data types, related to untrusted inputs to the SAX parsers. See GHSA-xh29-r2w5-wx8m for more information.

    Improvements

    • {HTML4,XML}::SAX::{Parser,ParserContext} constructor methods now raise TypeError instead of segfaulting when an incorrect type is passed.

    sha256:

    58417c7c10f78cd1c0e1984f81538300d4ea98962cfd3f46f725efee48f9757a  nokogiri-1.13.6-aarch64-linux.gem
    a2b04ec3b1b73ecc6fac619b41e9fdc70808b7a653b96ec97d04b7a23f158dbc  nokogiri-1.13.6-arm64-darwin.gem
    4437f2d03bc7da8854f4aaae89e24a98cf5c8b0212ae2bc003af7e65c7ee8e27  nokogiri-1.13.6-java.gem
    99d3e212bbd5e80aa602a1f52d583e4f6e917ec594e6aa580f6aacc253eff984  nokogiri-1.13.6-x64-mingw-ucrt.gem
    a04f6154a75b6ed4fe2d0d0ff3ac02f094b54e150b50330448f834fa5726fbba  nokogiri-1.13.6-x64-mingw32.gem
    a13f30c2863ef9e5e11240dd6d69ef114229d471018b44f2ff60bab28327de4d  nokogiri-1.13.6-x86-linux.gem
    63a2ca2f7a4f6bd9126e1695037f66c8eb72ed1e1740ef162b4480c57cc17dc6  nokogiri-1.13.6-x86-mingw32.gem
    2b266e0eb18030763277b30dc3d64337f440191e2bd157027441ac56a59d9dfe  nokogiri-1.13.6-x86_64-darwin.gem
    3fa37b0c3b5744af45f9da3e4ae9cbd89480b35e12ae36b5e87a0452e0b38335  nokogiri-1.13.6-x86_64-linux.gem
    b1512fdc0aba446e1ee30de3e0671518eb363e75fab53486e99e8891d44b8587  nokogiri-1.13.6.gem
    

    1.13.5 / 2022-05-04

    Security

    Dependencies

    • [CRuby] Vendored libxml2 is updated from v2.9.13 to v2.9.14.

    Improvements

    • [CRuby] The libxml2 HTML4 parser no longer exhibits quadratic behavior when recovering some broken markup related to start-of-tag and bare < characters.

    Changed

    • [CRuby] The libxml2 HTML4 parser in v2.9.14 recovers from some broken markup differently. Notably, the XML CDATA escape sequence <![CDATA[ and incorrectly-opened comments will result in HTML text nodes starting with &lt;! instead of skipping the invalid tag. This behavior is a direct result of the quadratic-behavior fix noted above. The behavior of downstream sanitizers relying on this behavior will also change. Some tests describing the changed behavior are in test/html4/test_comments.rb.

    ... (truncated)

    Changelog

    Sourced from nokogiri's changelog.

    1.13.6 / 2022-05-08

    Security

    • [CRuby] Address CVE-2022-29181, improper handling of unexpected data types, related to untrusted inputs to the SAX parsers. See GHSA-xh29-r2w5-wx8m for more information.

    Improvements

    • {HTML4,XML}::SAX::{Parser,ParserContext} constructor methods now raise TypeError instead of segfaulting when an incorrect type is passed.

    1.13.5 / 2022-05-04

    Security

    Dependencies

    • [CRuby] Vendored libxml2 is updated from v2.9.13 to v2.9.14.

    Improvements

    • [CRuby] The libxml2 HTML parser no longer exhibits quadratic behavior when recovering some broken markup related to start-of-tag and bare < characters.

    Changed

    • [CRuby] The libxml2 HTML parser in v2.9.14 recovers from some broken markup differently. Notably, the XML CDATA escape sequence <![CDATA[ and incorrectly-opened comments will result in HTML text nodes starting with &lt;! instead of skipping the invalid tag. This behavior is a direct result of the quadratic-behavior fix noted above. The behavior of downstream sanitizers relying on this behavior will also change. Some tests describing the changed behavior are in test/html4/test_comments.rb.

    1.13.4 / 2022-04-11

    Security

    Dependencies

    • [CRuby] Vendored zlib is updated from 1.2.11 to 1.2.12. (See LICENSE-DEPENDENCIES.md for details on which packages redistribute this library.)
    • [JRuby] Vendored Xerces-J (xerces:xercesImpl) is updated from 2.12.0 to 2.12.2.
    • [JRuby] Vendored nekohtml (org.cyberneko.html) is updated from a fork of 1.9.21 to 1.9.22.noko2. This fork is now publicly developed at https://github.com/sparklemotion/nekohtml

    ... (truncated)

    Commits
    • b7817b6 version bump to v1.13.6
    • 61b1a39 Merge pull request #2530 from sparklemotion/flavorjones-check-parse-memory-ty...
    • 83cc451 fix: {HTML4,XML}::SAX::{Parser,ParserContext} check arg types
    • 22c9e5b version bump to v1.13.5
    • 6155881 doc: update CHANGELOG for v1.13.5
    • c519a47 Merge pull request #2527 from sparklemotion/2525-update-libxml-2_9_14-v1_13_x
    • 66c2886 dep: update libxml2 to v2.9.14
    • b7c4cc3 test: unpend the LIBXML_LOADED_VERSION test on freebsd
    • eac7934 dev: require yaml
    • f3521ba style(rubocop): pend Style/FetchEnvVar for now
    • Additional commits viewable in compare view

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    dependencies 
    opened by dependabot[bot] 0
  • Changes in the hyperlinks in index.ipynb

    Changes in the hyperlinks in index.ipynb

    After downloading the repository and open it with jupyter notebook, clicking in the hyperlinks showed error 404, I think it's because they referred to the page in GitHub directly and not to a directory relative to index.ipynb. I changed all the links to refer relatively to index.ipynb instead of Github directly and now it's working for me.

    opened by daniel-tamayo 1
Owner
Diego Restrepo
Professor Insituto de Física Universidad de Antioquia
Diego Restrepo
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