From 396162c74d24426de54a7cbe0a3ad831c3b91d84 Mon Sep 17 00:00:00 2001 From: gagolews Date: Sat, 26 Dec 2020 20:22:18 +1100 Subject: [PATCH] v0.9.5 --- .github/workflows/py.yml | 2 +- .github/workflows/r.yml | 2 +- .gitignore | 1 - DESCRIPTION | 2 +- Makefile | 3 +- NEWS | 6 +- R/mst.R | 4 +- README.rst | 2 +- devel/sandbox_scanpy.py | 18 ++++-- devel/sphinx/index.rst | 2 + devel/sphinx/rapi/comparing_partitions.rst | 1 - devel/sphinx/rapi/gclust.rst | 1 - devel/sphinx/rapi/inequity.rst | 7 +- devel/sphinx/rapi/mst.rst | 1 - devel/testthat.R | 4 -- devel/tinytest.R | 4 ++ .../test-compare-partitions.R | 3 +- devel/{testthat => tinytest}/test-gclust.R | 5 +- devel/{testthat => tinytest}/test-inequity.R | 4 +- devel/{testthat => tinytest}/test-mst.R | 4 +- docs/_sources/index.rst.txt | 2 + .../rapi/comparing_partitions.rst.txt | 1 - docs/_sources/rapi/gclust.rst.txt | 1 - docs/_sources/rapi/inequity.rst.txt | 7 +- docs/_sources/rapi/mst.rst.txt | 1 - docs/_static/basic.css | 61 ++++++++++++------ docs/_static/doctools.js | 5 +- docs/_static/searchtools.js | 11 ++-- docs/genieclust_plots-1.pdf | Bin 8288 -> 8288 bytes docs/genieclust_plots-2.pdf | Bin 12135 -> 12135 bytes docs/genieclust_plots-3.pdf | Bin 7168 -> 7168 bytes docs/genieclust_plots-4.pdf | Bin 8830 -> 8830 bytes docs/rapi/inequity.html | 4 +- docs/searchindex.js | 2 +- setup.py | 2 +- 35 files changed, 99 insertions(+), 74 deletions(-) delete mode 100644 devel/testthat.R create mode 100644 devel/tinytest.R rename devel/{testthat => tinytest}/test-compare-partitions.R (96%) rename devel/{testthat => tinytest}/test-gclust.R (97%) rename devel/{testthat => tinytest}/test-inequity.R (92%) rename devel/{testthat => tinytest}/test-mst.R (97%) diff --git a/.github/workflows/py.yml b/.github/workflows/py.yml index 22ca87d3..21ce9e31 100644 --- a/.github/workflows/py.yml +++ b/.github/workflows/py.yml @@ -25,7 +25,7 @@ jobs: sudo apt-get update sudo apt-get -y upgrade sudo apt-get -y install libcurl4-openssl-dev python3-rpy2 libmlpack-dev r-base-dev python3-dev pandoc - sudo Rscript -e "install.packages(c('genie', 'Rcpp', 'devtools', 'testthat', 'emstreeR', 'knitr'))" + sudo Rscript -e "install.packages(c('genie', 'Rcpp', 'devtools', 'tinytest', 'emstreeR', 'knitr'))" sudo Rscript -e "devtools::install_github('gagolews/Rd2rst')" python -m pip install --upgrade pip if [ -f requirements.txt ]; then pip install -r requirements.txt --upgrade; fi diff --git a/.github/workflows/r.yml b/.github/workflows/r.yml index f2c71b63..f42cb78a 100644 --- a/.github/workflows/r.yml +++ b/.github/workflows/r.yml @@ -16,7 +16,7 @@ jobs: sudo apt-get update sudo apt-get -y upgrade sudo apt-get -y install libcurl4-openssl-dev python3-rpy2 libmlpack-dev r-base-dev - sudo Rscript -e "install.packages(c('genie', 'Rcpp', 'devtools', 'testthat', 'emstreeR'))" + sudo Rscript -e "install.packages(c('genie', 'Rcpp', 'devtools', 'tinytest', 'emstreeR'))" - name: Test and check R run: | sudo make r-test diff --git a/.gitignore b/.gitignore index 41d5dea4..62bcbbc4 100644 --- a/.gitignore +++ b/.gitignore @@ -21,4 +21,3 @@ cache-* coverage.xml .coverage htmlcov - diff --git a/DESCRIPTION b/DESCRIPTION index 83494571..e0694e71 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: genieclust Type: Package Title: The Genie++ Hierarchical Clustering Algorithm with Noise Points Detection Version: 0.9.5 -Date: 2020-09-23 +Date: 2020-12-26 Authors@R: c( person("Marek", "Gagolewski", role = c("aut", "cre", "cph"), diff --git a/Makefile b/Makefile index 4acc1399..4fee7ea2 100644 --- a/Makefile +++ b/Makefile @@ -60,8 +60,7 @@ r-check: r Rscript -e 'devtools::check(cran=TRUE, remote=TRUE, manual=TRUE)' r-test: r - Rscript -e 'options(width=120); source("devel/testthat.R")' - + Rscript -e 'options(width=120); source("devel/tinytest.R")' r-build: Rscript -e 'Rcpp::compileAttributes()' diff --git a/NEWS b/NEWS index 58dacc1e..eb61c1c1 100644 --- a/NEWS +++ b/NEWS @@ -1,10 +1,14 @@ # `genieclust` Package NEWS -## genieclust 0.9.5 (under development) +## genieclust 0.9.5 (2020-12-26) - [Python] `nmslib` is now required. +- [R] switched to `tinytest` for unit testing. + +- [R] fixed the examples that relied on a now-changed API of `emstreeR`. + ## genieclust 0.9.4 (2020-07-31) diff --git a/R/mst.R b/R/mst.R index c4cf0ece..f7986584 100644 --- a/R/mst.R +++ b/R/mst.R @@ -212,9 +212,9 @@ emst_mlpack <- function(X, verbose=FALSE) if (requireNamespace("emstreeR", quietly=TRUE)) { if (!verbose) - capture.output({mst <- emstreeR::mlpack_mst(X)}) + capture.output({mst <- emstreeR:::mlpack_mst(X)}) else - mst <- emstreeR::mlpack_mst(X) + mst <- emstreeR:::mlpack_mst(X) structure(t(mst), class="mst", diff --git a/README.rst b/README.rst index c9c9b863..1c25877e 100644 --- a/README.rst +++ b/README.rst @@ -48,7 +48,7 @@ difficult-to-set `eps` parameter. Author and Contributors ----------------------- -Author and Maintainer: `Marek Gagolewski `_ +Author and maintainer: `Marek Gagolewski `_ Contributors of the code from the original R package `genie`: `Anna Cena `_, diff --git a/devel/sandbox_scanpy.py b/devel/sandbox_scanpy.py index 7ed5658b..bee0acb7 100644 --- a/devel/sandbox_scanpy.py +++ b/devel/sandbox_scanpy.py @@ -10,6 +10,7 @@ import scanpy as sc sc.set_figure_params(dpi=100) ad = sc.datasets.pbmc3k() + sc.pp.filter_genes(ad, min_cells=10) ad.layers['counts'] = ad.X.copy() sc.pp.normalize_total(ad, target_sum=10000) @@ -17,10 +18,10 @@ sc.pp.highly_variable_genes(ad, n_top_genes=1000, flavor='seurat_v3', subset=True, layer='counts') sc.pp.scale(ad, max_value=8) sc.pp.pca(ad) + sc.pp.neighbors(ad) sc.tl.umap(ad) - sc.tl.louvain(ad, resolution=0.2) X_hidim = ad.X @@ -30,7 +31,7 @@ import genieclust import numpy as np -g = genieclust.Genie(n_clusters=3, affinity='cosine') +g = genieclust.Genie(n_clusters=4, affinity='cosine', M=25, postprocess="all") labels = g.fit_predict(X_hidim) ad.obs['genie_labels'] = labels.astype(str) sc.pl.umap(ad, color='genie_labels') @@ -43,12 +44,12 @@ sc.pl.umap(ad, color='louvain') -mst = genieclust.internal.mst_from_distance(X_hidim, 'cosine') +mst = genieclust.internal.mst_from_distance(X_hidim) genieclust.plots.plot_segments(mst[1], ad.obsm["X_umap"]) -X_hidim_std = (X_hidim-X_hidim.mean(axis=0))/(X_hidim.std(axis=0)) -g = genieclust.Genie(n_clusters=3, affinity='cosine', M=5, postprocess="merge") +X_hidim_std = (X_hidim-X_hidim.mean(axis=0))/(X_hidim.std(axis=0, ddof=1)) +g = genieclust.Genie(n_clusters=3) labels = g.fit_predict(X_hidim_std) ad.obs['genie_labels_std'] = labels.astype(str) sc.pl.umap(ad, color='genie_labels_std') @@ -63,3 +64,10 @@ #sc.pl.umap(ad, color='genie_labels') genieclust.plots.plot_segments(mst[1], ad.obsm["X_umap"]) + +from sklearn.decomposition import PCA +g = genieclust.Genie(n_clusters=3) +labels = g.fit_predict(PCA(20).fit_transform(X_hidim)) +ad.obs['genie_labels'] = labels.astype(str) +sc.pl.umap(ad, color='genie_labels') + diff --git a/devel/sphinx/index.rst b/devel/sphinx/index.rst index 1f3dbc78..c891d7b8 100644 --- a/devel/sphinx/index.rst +++ b/devel/sphinx/index.rst @@ -1,6 +1,8 @@ `genieclust`: Fast and Robust Hierarchical Clustering with Noise Point Detection ================================================================================ + + **Genie finds meaningful clusters and is fast even on large data sets.** -- by `Marek Gagolewski `_ diff --git a/devel/sphinx/rapi/comparing_partitions.rst b/devel/sphinx/rapi/comparing_partitions.rst index 6022ea0a..c8460f9d 100644 --- a/devel/sphinx/rapi/comparing_partitions.rst +++ b/devel/sphinx/rapi/comparing_partitions.rst @@ -87,4 +87,3 @@ Examples adjusted_mi_score(y_true, y_pred) normalized_accuracy(y_true, y_pred) pair_sets_index(y_true, y_pred) - diff --git a/devel/sphinx/rapi/gclust.rst b/devel/sphinx/rapi/gclust.rst index c34e9f40..62ca7561 100644 --- a/devel/sphinx/rapi/gclust.rst +++ b/devel/sphinx/rapi/gclust.rst @@ -147,4 +147,3 @@ Examples # Fast for low-dimensional Euclidean spaces: if (require("emstreeR")) h <- gclust(emst_mlpack(X)) - diff --git a/devel/sphinx/rapi/inequity.rst b/devel/sphinx/rapi/inequity.rst index 4c21a200..4d0b316b 100644 --- a/devel/sphinx/rapi/inequity.rst +++ b/devel/sphinx/rapi/inequity.rst @@ -18,9 +18,9 @@ Usage Arguments ~~~~~~~~~ -+-------+---------------------------------------+ -| ``x`` | numeric vector of non-negative values | -+-------+---------------------------------------+ +===== ===================================== +``x`` numeric vector of non-negative values +===== ===================================== Details ~~~~~~~ @@ -72,4 +72,3 @@ Examples bonferroni_index(c(0, 0, 10, 0, 0)) bonferroni_index(c(7, 0, 3, 0, 0)) bonferroni_index(c(6, 0, 3, 1, 0)) - diff --git a/devel/sphinx/rapi/mst.rst b/devel/sphinx/rapi/mst.rst index 58f77356..6fb7cc75 100644 --- a/devel/sphinx/rapi/mst.rst +++ b/devel/sphinx/rapi/mst.rst @@ -92,4 +92,3 @@ Examples data("iris") X <- iris[1:4] tree <- mst(X) - diff --git a/devel/testthat.R b/devel/testthat.R deleted file mode 100644 index fb45bf08..00000000 --- a/devel/testthat.R +++ /dev/null @@ -1,4 +0,0 @@ -set.seed(123) -library("testthat") -library("genieclust") -test_dir("devel/testthat/") diff --git a/devel/tinytest.R b/devel/tinytest.R new file mode 100644 index 00000000..f0d35d77 --- /dev/null +++ b/devel/tinytest.R @@ -0,0 +1,4 @@ +set.seed(123) +library("tinytest") +library("genieclust") +run_test_dir("devel/tinytest/") diff --git a/devel/testthat/test-compare-partitions.R b/devel/tinytest/test-compare-partitions.R similarity index 96% rename from devel/testthat/test-compare-partitions.R rename to devel/tinytest/test-compare-partitions.R index 2513046b..490a0d8c 100644 --- a/devel/testthat/test-compare-partitions.R +++ b/devel/tinytest/test-compare-partitions.R @@ -1,6 +1,5 @@ -library("testthat") +library("tinytest") library("genieclust") -context("compare-partitions") # More thorough tests are performed by pytest diff --git a/devel/testthat/test-gclust.R b/devel/tinytest/test-gclust.R similarity index 97% rename from devel/testthat/test-gclust.R rename to devel/tinytest/test-gclust.R index a964f48d..7c9e0ec9 100644 --- a/devel/testthat/test-gclust.R +++ b/devel/tinytest/test-gclust.R @@ -1,6 +1,5 @@ -library("testthat") +library("tinytest") library("genieclust") -context("gclust") verbose <- FALSE @@ -20,7 +19,7 @@ if (require("genie")) { #for (k in 2:20) expect_equal(adjusted_rand_score(cutree(h1, k), cutree(h2, k)), 1.0) } -if (require("emstreeR")) { +if (suppressMessages(require("emstreeR"))) { print(system.time(h2 <- gclust(emst_mlpack(X, verbose=verbose), verbose=verbose))) #for (k in 2:20) expect_equal(adjusted_rand_score(cutree(h1, k), cutree(h2, k)), 1.0) } diff --git a/devel/testthat/test-inequity.R b/devel/tinytest/test-inequity.R similarity index 92% rename from devel/testthat/test-inequity.R rename to devel/tinytest/test-inequity.R index b41ecc8b..f698deaf 100644 --- a/devel/testthat/test-inequity.R +++ b/devel/tinytest/test-inequity.R @@ -1,6 +1,6 @@ -library("testthat") +library("tinytest") library("genieclust") -context("inequity") + # More thorough tests are performed by pytest diff --git a/devel/testthat/test-mst.R b/devel/tinytest/test-mst.R similarity index 97% rename from devel/testthat/test-mst.R rename to devel/tinytest/test-mst.R index 2fb1c56b..45abad1c 100644 --- a/devel/testthat/test-mst.R +++ b/devel/tinytest/test-mst.R @@ -1,6 +1,6 @@ -library("testthat") +library("tinytest") library("genieclust") -context("mst") + set.seed(123) diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt index 1f3dbc78..c891d7b8 100644 --- a/docs/_sources/index.rst.txt +++ b/docs/_sources/index.rst.txt @@ -1,6 +1,8 @@ `genieclust`: Fast and Robust Hierarchical Clustering with Noise Point Detection ================================================================================ + + **Genie finds meaningful clusters and is fast even on large data sets.** -- by `Marek Gagolewski `_ diff --git a/docs/_sources/rapi/comparing_partitions.rst.txt b/docs/_sources/rapi/comparing_partitions.rst.txt index 6022ea0a..c8460f9d 100644 --- a/docs/_sources/rapi/comparing_partitions.rst.txt +++ b/docs/_sources/rapi/comparing_partitions.rst.txt @@ -87,4 +87,3 @@ Examples adjusted_mi_score(y_true, y_pred) normalized_accuracy(y_true, y_pred) pair_sets_index(y_true, y_pred) - diff --git a/docs/_sources/rapi/gclust.rst.txt b/docs/_sources/rapi/gclust.rst.txt index c34e9f40..62ca7561 100644 --- a/docs/_sources/rapi/gclust.rst.txt +++ b/docs/_sources/rapi/gclust.rst.txt @@ -147,4 +147,3 @@ Examples # Fast for low-dimensional Euclidean spaces: if (require("emstreeR")) h <- gclust(emst_mlpack(X)) - diff --git a/docs/_sources/rapi/inequity.rst.txt b/docs/_sources/rapi/inequity.rst.txt index 4c21a200..4d0b316b 100644 --- a/docs/_sources/rapi/inequity.rst.txt +++ b/docs/_sources/rapi/inequity.rst.txt @@ -18,9 +18,9 @@ Usage Arguments ~~~~~~~~~ -+-------+---------------------------------------+ -| ``x`` | numeric vector of non-negative values | -+-------+---------------------------------------+ +===== ===================================== +``x`` numeric vector of non-negative values +===== ===================================== Details ~~~~~~~ @@ -72,4 +72,3 @@ Examples bonferroni_index(c(0, 0, 10, 0, 0)) bonferroni_index(c(7, 0, 3, 0, 0)) bonferroni_index(c(6, 0, 3, 1, 0)) - diff --git a/docs/_sources/rapi/mst.rst.txt b/docs/_sources/rapi/mst.rst.txt index 58f77356..6fb7cc75 100644 --- a/docs/_sources/rapi/mst.rst.txt +++ b/docs/_sources/rapi/mst.rst.txt @@ -92,4 +92,3 @@ Examples data("iris") X <- iris[1:4] tree <- mst(X) - diff --git a/docs/_static/basic.css b/docs/_static/basic.css index 56f5efc6..24a49f09 100644 --- a/docs/_static/basic.css +++ b/docs/_static/basic.css @@ -15,6 +15,12 @@ div.clearer { clear: both; } +div.section::after { + display: block; + content: ''; + clear: left; +} + /* -- relbar ---------------------------------------------------------------- */ div.related { @@ -328,8 +334,8 @@ p.sidebar-title { font-weight: bold; } -div.admonition, div.topic, pre, div[class|="highlight"] { - clear: both; +div.admonition, div.topic, blockquote { + clear: left; } /* -- topics ---------------------------------------------------------------- */ @@ -338,7 +344,6 @@ div.topic { border: 1px solid #ccc; padding: 7px; margin: 10px 0 10px 0; - overflow-x: auto; } p.topic-title { @@ -353,7 +358,6 @@ div.admonition { margin-top: 10px; margin-bottom: 10px; padding: 7px; - overflow-x: auto; } div.admonition dt { @@ -378,6 +382,15 @@ div.admonition > :last-child { margin-bottom: 0; } +div.sidebar::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + /* -- tables ---------------------------------------------------------------- */ table.docutils { @@ -513,28 +526,31 @@ ol.upperroman { list-style: upper-roman; } -ol > li:first-child > :first-child, -ul > li:first-child > :first-child { +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { margin-top: 0px; } -ol ol > li:first-child > :first-child, -ol ul > li:first-child > :first-child, -ul ol > li:first-child > :first-child, -ul ul > li:first-child > :first-child { - margin-top: revert; +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; } -ol > li:last-child > :last-child, -ul > li:last-child > :last-child { - margin-bottom: 0px; +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; } -ol ol > li:last-child > :last-child, -ol ul > li:last-child > :last-child, -ul ol > li:last-child > :last-child, -ul ul > li:last-child > :last-child { - margin-bottom: revert; +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; } dl.footnote > dt, @@ -677,6 +693,10 @@ pre { overflow-y: hidden; /* fixes display issues on Chrome browsers */ } +pre, div[class*="highlight-"] { + clear: both; +} + span.pre { -moz-hyphens: none; -ms-hyphens: none; @@ -684,7 +704,7 @@ span.pre { hyphens: none; } -div[class^="highlight-"] { +div[class*="highlight-"] { margin: 1em 0; } @@ -744,6 +764,7 @@ div.code-block-caption code { } table.highlighttable td.linenos, +span.linenos, div.doctest > div.highlight span.gp { /* gp: Generic.Prompt */ user-select: none; } diff --git a/docs/_static/doctools.js b/docs/_static/doctools.js index daccd209..7d88f807 100644 --- a/docs/_static/doctools.js +++ b/docs/_static/doctools.js @@ -285,9 +285,10 @@ var Documentation = { initOnKeyListeners: function() { $(document).keydown(function(event) { var activeElementType = document.activeElement.tagName; - // don't navigate when in search box or textarea + // don't navigate when in search box, textarea, dropdown or button if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT' - && !event.altKey && !event.ctrlKey && !event.metaKey && !event.shiftKey) { + && activeElementType !== 'BUTTON' && !event.altKey && !event.ctrlKey && !event.metaKey + && !event.shiftKey) { switch (event.keyCode) { case 37: // left var prevHref = $('link[rel="prev"]').prop('href'); diff --git a/docs/_static/searchtools.js b/docs/_static/searchtools.js index ab564996..261ecaa9 100644 --- a/docs/_static/searchtools.js +++ b/docs/_static/searchtools.js @@ -59,10 +59,10 @@ var Search = { _pulse_status : -1, htmlToText : function(htmlString) { - var htmlElement = document.createElement('span'); - htmlElement.innerHTML = htmlString; - $(htmlElement).find('.headerlink').remove(); - docContent = $(htmlElement).find('[role=main]')[0]; + var virtualDocument = document.implementation.createHTMLDocument('virtual'); + var htmlElement = $(htmlString, virtualDocument); + htmlElement.find('.headerlink').remove(); + docContent = htmlElement.find('[role=main]')[0]; if(docContent === undefined) { console.warn("Content block not found. Sphinx search tries to obtain it " + "via '[role=main]'. Could you check your theme or template."); @@ -166,8 +166,7 @@ var Search = { objectterms.push(tmp[i].toLowerCase()); } - if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i].match(/^\d+$/) || - tmp[i] === "") { + if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i] === "") { // skip this "word" continue; } diff --git a/docs/genieclust_plots-1.pdf b/docs/genieclust_plots-1.pdf index a3a92812433fcb66cbb2078a0c54de6db674c5af..62eb5525bdcc8a5abdfca4cf8bd50654be117955 100644 GIT binary patch delta 23 fcmaFh@W5fi5?L-oBO@~-10w@t4k&&5^fsui+$z~O8XBGfsLI%kI delta 23 ecmaDJ_dITcls1=vg`v5jiLr@+(PkBGXBGfss|L{k diff --git a/docs/genieclust_plots-3.pdf b/docs/genieclust_plots-3.pdf index 5aba1ec50d08b30e7f38e4c9105a28b4a47fd7bd..4e5e9546c3b53c9e168410eb17b35628b0c92681 100644 GIT binary patch delta 23 ecmZp$Xt3CjBgtiGWMpP!U}RuyvbjvMiwOWxf(CQ| delta 23 ecmZp$Xt3CjBgti8VQ6k>Vr*hyytz!WiwOWx@dkYW diff --git a/docs/genieclust_plots-4.pdf b/docs/genieclust_plots-4.pdf index 7b624fe4f8e2cbe155d6e7238b9cc7dc88777d8d..95ea472747edf2fec7f6b378ae69d41ebcc8e728 100644 GIT binary patch delta 23 fcmez8^3P?%HF+*WBO@~-10w@tlg$t0=P>~Qa^47h delta 23 fcmez8^3P?%HF+)r3qx~56Jrwt~Qb4>_^ diff --git a/docs/rapi/inequity.html b/docs/rapi/inequity.html index f9441e0b..19def605 100644 --- a/docs/rapi/inequity.html +++ b/docs/rapi/inequity.html @@ -228,8 +228,8 @@

Usage

ArgumentsΒΆ

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Package genieclust Reference","genieclust.compare_partitions","genieclust.Genie","genieclust.inequity","genieclust.internal","genieclust.plots","genieclust.tools","genieclust: Fast and Robust Hierarchical Clustering with Noise Point Detection","R Package genieclust Reference","comparing_partitions: Pairwise Partition Similarity Scores","emst_mlpack: Euclidean Minimum Spanning Tree","gclust: The Genie++ Hierarchical Clustering Algorithm","genieclust-package: The Genie++ Hierarchical Clustering Algorithm (with Extras)","inequity: Inequity (Inequality) Measures","mst: Minimum Spanning Tree of the Pairwise Distance Graph","Basics","Benchmarks \u2014 Approximate Method","Benchmarks (How Good Is It?)","Benchmarks \u2014 Detailed Results","Clustering with Noise Points Detection","R Interface Examples","Comparing Algorithms on Toy Datasets","Example: Sparse Data and Movie Recommendation","Example: String Data and Grouping of DNA","Timings (How Fast Is 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\ No newline at end of file diff --git a/setup.py b/setup.py index 8c7c0b88..1b53bae6 100644 --- a/setup.py +++ b/setup.py @@ -135,7 +135,7 @@ def build_extensions(self): setuptools.setup( name="genieclust", - version="0.9.5.dev0", # see also genieclust/__init__.py; e.g., 0.9.4.dev0 + version="0.9.5", # see also genieclust/__init__.py; e.g., 0.9.4.dev0 description="The Genie++ Hierarchical Clustering Algorithm (with Extras)", long_description=long_description, long_description_content_type="text/x-rst",

x