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Finish conversion from sicmutils (#2)
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‎.clj-kondo/config.edn

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{:linters {:unresolved-symbol {:level :off}
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:invalid-arity {:level :off}}}
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:config-paths ["../resources/clj-kondo.exports/emmy/emmy"
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:config-paths ["../resources/clj-kondo.exports/org.mentat/emmy"
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"com.gfredericks/test.chuck"]
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:output {:exclude-files ["src/data_readers.clj"]}

‎.cljfmt.edn

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{:indentation? false
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:sort-ns-references? true}

‎CHANGELOG.md

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‎CITATION.cff

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version: 0.23.0
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date-released: 2016
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type: software
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url: "https://github.com/emmy/emmy"
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url: "https://github.com/mentat-collective/emmy"
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license: GPL-3.0
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license-url: "https://www.gnu.org/licenses/gpl-3.0.en.html"
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repository-code: "https://github.com/emmy/emmy"
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repository-code: "https://github.com/mentat-collective/emmy"

‎README.md

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Emmy provides facilities for
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- [symbolic
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computation](https://cljdoc.org/d/emmy/emmy/CURRENT/doc/data-types/symbolic-expressions),
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computation](https://cljdoc.org/d/org.mentat/emmy/CURRENT/doc/data-types/symbolic-expressions),
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including state of the art TeX rendering and [expression
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simplification](https://cljdoc.org/d/emmy/emmy/CURRENT/doc/simplification)
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- [automatic](https://cljdoc.org/d/emmy/emmy/CURRENT/doc/calculus/automatic-differentiation),
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[numerical](https://cljdoc.org/d/emmy/emmy/CURRENT/doc/numerical-methods/numerical-derivative)
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simplification](https://cljdoc.org/d/org.mentat/emmy/CURRENT/doc/simplification)
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- [automatic](https://cljdoc.org/d/org.mentat/emmy/CURRENT/doc/calculus/automatic-differentiation),
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[numerical](https://cljdoc.org/d/org.mentat/emmy/CURRENT/doc/numerical-methods/numerical-derivative)
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and
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[symbolic](https://cljdoc.org/d/emmy/emmy/CURRENT/doc/calculus/automatic-differentiation)
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[symbolic](https://cljdoc.org/d/org.mentat/emmy/CURRENT/doc/calculus/automatic-differentiation)
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differentiation
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- [numerical integration and
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optimization](https://cljdoc.org/d/emmy/emmy/CURRENT/doc/numerical-methods)
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optimization](https://cljdoc.org/d/org.mentat/emmy/CURRENT/doc/numerical-methods)
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- investigations in [differential
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geometry](https://cljdoc.org/d/emmy/emmy/CURRENT/doc/textbooks/functional-differential-geometry)
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geometry](https://cljdoc.org/d/org.mentat/emmy/CURRENT/doc/textbooks/functional-differential-geometry)
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and [Lagrangian and Hamiltonian
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mechanics](https://cljdoc.org/d/emmy/emmy/CURRENT/doc/textbooks/structure-and-interpretation-of-classical-mechanics)
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mechanics](https://cljdoc.org/d/org.mentat/emmy/CURRENT/doc/textbooks/structure-and-interpretation-of-classical-mechanics)
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And implementations of many different [mathematical
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objects](https://cljdoc.org/d/emmy/emmy/CURRENT/doc/data-types), all
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objects](https://cljdoc.org/d/org.mentat/emmy/CURRENT/doc/data-types), all
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built on a tower of [generic, extensible mathematical
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operations](https://cljdoc.org/d/emmy/emmy/CURRENT/doc/basics/generics).
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operations](https://cljdoc.org/d/org.mentat/emmy/CURRENT/doc/basics/generics).
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Scmutils is extensively used in the textbooks [The Structure and Interpretation
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of Classical Mechanics][SICM] and [Functional Differential Geometry][FDG] by
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> Slack](http://clojurians.net/) in
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> [#emmy](https://clojurians.slack.com/archives/C01ECA9AA74).
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[![Build Status](https://github.com/emmy/emmy/workflows/Clojure%20CI/badge.svg?branch=main)](https://github.com/emmy/emmy/actions?query=workflow%3A%22Clojure+CI%22)
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[![License](https://img.shields.io/badge/license-GPLv3-brightgreen.svg)](https://github.com/emmy/emmy/blob/main/LICENSE)
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[![Codecov branch](https://img.shields.io/codecov/c/github/emmy/emmy/main.svg?maxAge=3600)](https://codecov.io/github/emmy/emmy)
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[![cljdoc badge](https://cljdoc.org/badge/emmy/emmy)](https://cljdoc.org/d/emmy/emmy/CURRENT)
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[![Clojars Project](https://img.shields.io/clojars/v/emmy/emmy.svg)](https://clojars.org/emmy/emmy)
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[![Build Status](https://github.com/mentat-collective/emmy/workflows/Clojure%20CI/badge.svg?branch=main)](https://github.com/mentat-collective/emmy/actions?query=workflow%3A%22Clojure+CI%22)
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[![License](https://img.shields.io/badge/license-GPLv3-brightgreen.svg)](https://github.com/mentat-collective/emmy/blob/main/LICENSE)
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[![Codecov branch](https://img.shields.io/codecov/c/github/mentat-collective/emmy/main.svg?maxAge=3600)](https://codecov.io/github/mentat-collective/emmy)
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[![cljdoc badge](https://cljdoc.org/badge/org.mentat/emmy)](https://cljdoc.org/d/org.mentat/emmy/CURRENT)
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[![Clojars Project](https://img.shields.io/clojars/v/org.mentat/emmy.svg)](https://clojars.org/org.mentat/emmy)
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## Quickstart
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> Emmy is best experienced in an interactive environment like the
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> [REPL](https://clojure.org/guides/repl/introduction). We [support many
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> environments](https://cljdoc.org/d/emmy/emmy/CURRENT/doc/basics/how-to-use-emmy)
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> environments](https://cljdoc.org/d/org.mentat/emmy/CURRENT/doc/basics/how-to-use-emmy)
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> with rich support for [TeX](https://en.wikipedia.org/wiki/TeX) rendering and
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> plotting.
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Install Emmy into your Clojure(script) project using the instructions at
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its Clojars page:
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[![Clojars Project](https://img.shields.io/clojars/v/emmy/emmy.svg)](https://clojars.org/emmy/emmy)
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[![Clojars Project](https://img.shields.io/clojars/v/org.mentat/emmy.svg)](https://clojars.org/org.mentat/emmy)
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Initialize the `emmy.env` "Batteries Included" environment at the REPL:
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<img width="1152" alt="nje" src="https://user-images.githubusercontent.com/462255/109587851-9e1be280-7abc-11eb-9369-6d56519fb3cd.png">
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Math works as expected (see
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[Generics](https://cljdoc.org/d/emmy/emmy/CURRENT/doc/basics/generics)
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[Generics](https://cljdoc.org/d/org.mentat/emmy/CURRENT/doc/basics/generics)
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for the full menu of operations), but notice that the numeric tower includes
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[complex
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numbers](https://cljdoc.org/d/emmy/emmy/CURRENT/doc/data-types/complex),
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numbers](https://cljdoc.org/d/org.mentat/emmy/CURRENT/doc/data-types/complex),
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and proper ratios in ClojureScript:
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```clojure
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Symbols are interpreted as abstract complex numbers, and arithmetic on them
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generates symbolic expressions. You can render these with
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[`->TeX`](https://cljdoc.org/d/emmy/emmy/CURRENT/api/emmy.expression.render#->TeX)
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[`->TeX`](https://cljdoc.org/d/org.mentat/emmy/CURRENT/api/emmy.expression.render#->TeX)
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and
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[`->infix`](https://cljdoc.org/d/emmy/emmy/CURRENT/api/emmy.expression.render#->infix):
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[`->infix`](https://cljdoc.org/d/org.mentat/emmy/CURRENT/api/emmy.expression.render#->infix):
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```clojure
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(def render (comp ->infix simplify))
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```
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Use the
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[`D`](https://cljdoc.org/d/emmy/emmy/CURRENT/api/emmy.calculus.derivative#D)
105+
[`D`](https://cljdoc.org/d/org.mentat/emmy/CURRENT/api/emmy.calculus.derivative#D)
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operator to perform [forward-mode automatic
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differentiation](https://cljdoc.org/d/emmy/emmy/CURRENT/doc/calculus/automatic-differentiation)
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differentiation](https://cljdoc.org/d/org.mentat/emmy/CURRENT/doc/calculus/automatic-differentiation)
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and
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[`simplify`](https://cljdoc.org/d/emmy/emmy/CURRENT/doc/simplification)
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[`simplify`](https://cljdoc.org/d/org.mentat/emmy/CURRENT/doc/simplification)
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to collapse symbolic expressions into tidy form:
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```clojure
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license = {GPL-3.0},
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month = {4},
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title = {{Emmy: Functional Computer Algebra in Clojure}},
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url = {https://github.com/emmy/emmy},
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url = {https://github.com/mentat-collective/emmy},
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version = {0.23.0},
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year = {2016}
218218
```
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[GPL v3](LICENSE).
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[CLJDOCS]: https://cljdoc.org/d/emmy/emmy/CURRENT
228+
[CLJDOCS]: https://cljdoc.org/d/org.mentat/emmy/CURRENT
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[SICM]: https://mitpress.mit.edu/books/structure-and-interpretation-classical-mechanics-second-edition
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[FDG]: http://mitpress.mit.edu/books/functional-differential-geometry
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[SICP]: http://mitpress.mit.edu/sicp/
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[GSCM]: http://www.cs.rochester.edu/~gildea/guile-scmutils/
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[REFMAN]: https://cljdoc.org/d/emmy/emmy/CURRENT/doc/reference-manual
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[REFMAN]: https://cljdoc.org/d/org.mentat/emmy/CURRENT/doc/reference-manual
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[PHYSICS_IN_CLOJURE]: https://www.youtube.com/watch?v=7PoajCqNKpg
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Copyright © 2016 Colin Smith

‎bb.edn

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{:pods {clj-kondo/clj-kondo {:version "2022.12.10"}}
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:tasks
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{:requires ([pod.borkdude.clj-kondo :as clj-kondo])
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test:clj
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{:doc "Run CLJ tests."
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:task (shell "clojure -X:test:runner")}
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test:cljs
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{:doc "Run CLJS tests."
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:task (shell "npm run test")}
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release
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{:doc "Release the library to Clojars."
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:task (shell "clojure -T:build publish")}
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lint
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{:doc "Lint with clj-kondo."
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:task (clj-kondo/print!
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(clj-kondo/run! {:lint ["src" "test"]}))}}}

‎build.clj

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;; ## Variables
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(def lib 'emmy/emmy)
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(def lib 'org.mentat/emmy)
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(def version (slurp "resources/EMMY_VERSION"))
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(defn- ->version
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[{:keys [version-suffix] :as opts}]
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(let [version (->version version-suffix)
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jar-file (->jar-file version)]
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(b/write-pom {:class-dir class-dir
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:lib lib
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:version version
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:scm {:tag (str "v" version)}
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:basis basis
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:src-pom "template/pom.xml"
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:src-dirs ["src"]
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:resource-dirs ["resources"]})
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(b/write-pom
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{:class-dir class-dir
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:lib lib
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:version version
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:scm
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{:tag (str "v" version)
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:connection "scm:git:git://github.com/mentat-collective/emmy.git"
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:developConnection "scm:git:ssh://[email protected]/mentat-collect/emmy.git"
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:url "https://github.com/mentat-collective/emmy"}
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:basis basis
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:src-pom "template/pom.xml"
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:src-dirs ["src"]
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:resource-dirs ["resources"]})
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(doseq [f ["README.md" "LICENSE" "deps.edn"]]
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(b/copy-file {:src f :target (format "%s/%s" class-dir f)}))
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(b/copy-dir {:src-dirs ["src" "resources"]

‎doc/basics/using_sicmutils.adoc

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= How to Use Emmy
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:uri-QUICKSTART: https://github.com/emmy/emmy#quickstart
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:uri-QUICKSTART: https://github.com/mentat-collective/emmy#quickstart
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== Emmy Supported Environments
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Install Emmy into your Clojure(script) project using the instructions at
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its Clojars page:
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image::https://img.shields.io/clojars/v/emmy/emmy.svg[caption="Emmy Clojars Project", link="https://clojars.org/emmy/emmy"]
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image::https://img.shields.io/clojars/v/org.mentat/emmy.svg[caption="Emmy Clojars Project", link="https://clojars.org/org.mentat/emmy"]
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Initialize the `emmy.env` "Batteries Included" environment at the REPL:
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----
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Any subsequent ClojureScript block will have every function in
54-
https://cljdoc.org/d/emmy/emmy/CURRENT/api/emmy.env[``emmy.env``]
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https://cljdoc.org/d/org.mentat/emmy/CURRENT/api/emmy.env[``emmy.env``]
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available.
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Visit the https://nextjournal.com/try/samritchie/emmy[Emmy Tutorial on

‎doc/calculus/autodiff.adoc

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NOTE: This note about conditionals is currently true in Emmy, but we're
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working on it. See
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https://github.com/emmy/emmy/issues/191[this ticket] for
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https://github.com/mentat-collective/emmy/issues/191[this ticket] for
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information on the plan to make generic comparisons in conditionals work in
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automatic differentiation.
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‎doc/contributing.adoc

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https://github.com/cloverage/cloverage[Cloverage] generates coverage reports for
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every pull request and the main branch in the repository. Coverage reports live
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at https://codecov.io/github/emmy/emmy[codecov.io].
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at https://codecov.io/github/mentat-collective/emmy[codecov.io].
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To invoke cloverage, call
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‎doc/faq.adoc

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=== How should I configure Emacs?
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The Emmy repository includes a
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https://github.com/emmy/emmy/blob/main/.dir-locals.el[dir-locals.el]
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https://github.com/mentat-collective/emmy/blob/main/.dir-locals.el[dir-locals.el]
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file with a few variable settings that improve the Emacs experience with
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Emmy.
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automatically simplify forms before rendering them.
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``expression->stream`` currently uses ``clojure.pprint`` to print simplified
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values. Once https://github.com/emmy/emmy/issues/519[#519] is
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values. Once https://github.com/mentat-collective/emmy/issues/519[#519] is
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completed, the ``pprint`` call will be replaced by a call you can bind to
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``prn``, ``zprint`` or any other preferred printer.

‎doc/intro.adoc

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@@ -20,17 +20,17 @@ TIP: Need help getting started? Say hi on https://twitter.com/sritchie[Twitter]
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or http://clojurians.net/[Clojurians Slack] in
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https://clojurians.slack.com/archives/C01ECA9AA74[#emmy].
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image:https://github.com/emmy/emmy/workflows/Clojure%20CI/badge.svg?branch=main[Build Status, link=https://github.com/emmy/emmy/actions?query=workflow%3A%22Clojure+CI%22]
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image:https://img.shields.io/codecov/c/github/emmy/emmy/main.svg?maxAge=3600[Codecov branch, link=https://codecov.io/github/emmy/emmy]
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image:https://cljdoc.org/badge/emmy/emmy[cljdoc badge, link=https://cljdoc.org/d/emmy/emmy/CURRENT]
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image:https://img.shields.io/clojars/v/emmy/emmy.svg[Clojars Project, link=https://clojars.org/emmy/emmy]
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image:https://github.com/mentat-collective/emmy/workflows/Clojure%20CI/badge.svg?branch=main[Build Status, link=https://github.com/mentat-collective/emmy/actions?query=workflow%3A%22Clojure+CI%22]
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image:https://img.shields.io/codecov/c/github/mentat-collective/emmy/main.svg?maxAge=3600[Codecov branch, link=https://codecov.io/github/mentat-collective/emmy]
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image:https://cljdoc.org/badge/org.mentat/emmy[cljdoc badge, link=https://cljdoc.org/d/org.mentat/emmy/CURRENT]
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image:https://img.shields.io/clojars/v/org.mentat/emmy.svg[Clojars Project, link=https://clojars.org/org.mentat/emmy]
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== Quickstart
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3030
Install Emmy into your Clojure(script) project using the instructions at
3131
its Clojars page:
3232

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image::https://img.shields.io/clojars/v/emmy/emmy.svg[Clojars Project, link=https://clojars.org/emmy/emmy]
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image::https://img.shields.io/clojars/v/org.mentat/emmy.svg[Clojars Project, link=https://clojars.org/org.mentat/emmy]
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Initialize a REPL and simplify a trigonometric identity:
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‎doc/linters.md

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To install the exported linter configuration:
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1. Install the Emmy dependency into your project using the appropriate
38-
entry listed at [Clojars](https://clojars.org/emmy). For example, If you
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1. Install the Emmy dependency into your project using the appropriate entry
38+
listed at [Clojars](https://clojars.org/org.mentat/emmy). For example, If you
3939
are using `deps.edn`, add the project to the map under `:deps`:
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```clj
42-
;; See https://clojars.org/emmy to pick an explicit version!
42+
;; See https://clojars.org/org.mentat/emmy to pick an explicit version!
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{:deps
44-
{emmy/emmy {:mvn/version "RELEASE"}}
44+
{org.mentat/emmy {:mvn/version "RELEASE"}}
4545
```
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2. Install clj-kondo using [these
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```shellsession
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# If you're using Leiningen:
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$ clj-kondo --copy-configs --dependencies --lint "$(lein classpath)"
66-
Imported config to .clj-kondo/emmy/emmy. To activate, add "emmy/emmy" to :config-paths in .clj-kondo/config.edn.
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Imported config to .clj-kondo/org.mentat/emmy. To activate, add "org.mentat/emmy" to :config-paths in .clj-kondo/config.edn.
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# If you're using deps.edn:
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$ clj-kondo --copy-configs --dependencies --lint "$(clojure -Spath)"
70-
Imported config to .clj-kondo/emmy/emmy. To activate, add "emmy/emmy" to :config-paths in .clj-kondo/config.edn.
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Imported config to .clj-kondo/org.mentat/emmy. To activate, add "org.mentat/emmy" to :config-paths in .clj-kondo/config.edn.
7171
```
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5. As instructed, either create or edit `.clj-kondo/config.edn` so that it contains a `:config-paths` entry with `"emmy/emmy"`:
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5. As instructed, either create or edit `.clj-kondo/config.edn` so that it
74+
contains a `:config-paths` entry with `"org.mentat/emmy"`:
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```clj
76-
{:config-paths ["emmy/emmy"]}
77+
{:config-paths ["org.mentat/emmy"]}
7778
```
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6. Check the imported files into source control in your project.

‎doc/numerical/multimin.adoc

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----
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See
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https://github.com/emmy/emmy/blob/main/src/emmy/numerical/multimin/nelder_mead.cljc#L238[the
89+
https://github.com/mentat-collective/emmy/blob/main/src/emmy/numerical/multimin/nelder_mead.cljc#L238[the
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documentation for `nelder-mead`] for the full menu of options and an accounting
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of the available defaults.
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WARNING: The following section describes algorithms that aren't yet implemented
9494
in Emmy. If you need these, please
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https://github.com/emmy/emmy/pulls[file an issue] and we can
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https://github.com/mentat-collective/emmy/pulls[file an issue] and we can
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help you get started.
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If we know more than just the function to minimize we can use that information

‎doc/numerical/ode.adoc

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@@ -24,7 +24,7 @@ used can be set by the user:
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WARNING: In Emmy we currently only support the Gragg-Bulirsch-Stoer
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algorithm. If you need any of the others, please
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https://github.com/emmy/emmy/pulls[file a PR] and we can
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https://github.com/mentat-collective/emmy/pulls[file a PR] and we can
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discuss how to get these in for you.
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The integration methods all automatically select the step sizes to maintain the

‎doc/numerical/quadrature.adoc

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@@ -26,7 +26,7 @@ Optionally you can supply a map of keyword arguments. The top level
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of the definite integral.
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* `*:method*`: Specifies the integration method used. Must be:
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** a keyword naming one of the available methods in
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https://github.com/emmy/emmy/blob/1aa81540a8109199ad111bde6ed5021624e62b73/src/emmy/numerical/quadrature.cljc#L65[`available-methods`]
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https://github.com/mentat-collective/emmy/blob/1aa81540a8109199ad111bde6ed5021624e62b73/src/emmy/numerical/quadrature.cljc#L65[`available-methods`]
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** a function with the proper integrator signature
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** a dictionary of integrator options with a `:method` key
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‎doc/numerical/unimin.adoc

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@@ -33,7 +33,7 @@ into how Brent's method works. It turns out there is a long history of this
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algorithm being cargo-culted along from library to library. I (@sritchie) now
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_do_ understand Brent's method, and I've tried to disgorge that understanding
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into the
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https://github.com/emmy/emmy/blob/main/src/emmy/numerical/unimin/brent.cljc[`emmy.numerical.unimin.brent`]
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https://github.com/mentat-collective/emmy/blob/main/src/emmy/numerical/unimin/brent.cljc[`emmy.numerical.unimin.brent`]
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namespace. Expect this to get better over time.
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The actual procedure in the system is:
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NOTE: The following section describing `local-minima` and `local-maxima` does
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not yet work. A port of this work is in progress at
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https://github.com/emmy/emmy/pull/108[this PR], if you'd like
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https://github.com/mentat-collective/emmy/pull/108[this PR], if you'd like
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to follow along.
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We can find a number of local minima of a multimodal function using a search

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