From d643d47d626ea822afee8c545518a976d66bec93 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Mon, 24 Mar 2025 21:07:25 +0000
Subject: [PATCH] chore: release 1.0.0

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+# Changelog
+
+## 1.0.0 (2025-03-24)
+
+
+### Features
+
+* add collapsed-tree support calculations via gotree rules ([6391a79](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/6391a79b7e7fedbd5ad3757ede0d3bb4a225a56d))
+* add further plots to compare across models and missingness ([e8cebab](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/e8cebab5c1c36bb06daeb11f72e4681892dc2b6e))
+* also look at consensus tree of all maximum likelihood trees ([33c2dd7](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/33c2dd70ce01a7a4bd0ee07fe2a65220c39ceaea))
+* clean up and improve max_missing topologies summary plot ([70cd27d](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/70cd27dacd4444f238fccafac02a3809f48245c9))
+* complete cluster_info_dist.R script ([cce6e1d](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/cce6e1da2a9116710d1e8cf504c861b1a03e279d))
+* compute and plot cluster information distance for all relevant tree sets ([9917ebb](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/9917ebbb81195cd3a8b5fa9d98c1da44bcefd7c4))
+* generate and collect bootstrap convergence and rfdist metrics ([ff634fb](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/ff634fb892285962236405f7ebbd150ced066cdf))
+* implement cluster selection and qc for more focused consensus tree ([2bf3be7](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/2bf3be710febf00fb98e0e747028bbdc595a1d6b))
+* implement consensus tree building from CID cluster among mlTrees with highest average likelihood ([c3eff03](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/c3eff03c509ad54be07a0bb3fe838656c09ef851))
+* improve error messages backtraces in cluster_info_dist.R ([5497d31](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/5497d31dbbb0aeb97c40ce2474e58e69c716a086))
+* overhaul summary plots (add information criteria, add ecdf and histogram plots) ([7f111f6](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/7f111f6c773470c8b6a6421b9d7c333168a5e2f5))
+* switch axes and facet labels in large overview plots ([89183f7](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/89183f72f6a4b3a651c610bc5992aaf79c8d4f49))
+
+
+### Bug Fixes
+
+* adjust file name downstream of previous change ([4ef281d](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/4ef281dd04973e7d45f24c24047db8ade91c0626))
+* adjust file name extraction pattern ([7cf439e](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/7cf439e77cd8343dedac86b853548e54b49b2362))
+* allow big plots ([e79a8ce](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/e79a8ce27994ad93ddd4cc7e744a1a2847869839))
+* always compute support based on raxml-ng bootstraps with gotree ([8b08105](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/8b081059bac1192c23f86a3573298e4ed49bdcb8))
+* amend previous commit ([441d5c5](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/441d5c5522f1d54e31b89369bda4eb4b7d243da6))
+* better error backtrace ([7ebc0bb](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/7ebc0bb3b0149959fce8a7f89fbf6ecaa7b8c0c6))
+* file path and resources adjustments ([04e63ef](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/04e63efa196452607b939ea593c4056bfd18aa54))
+* hard-coded output file names will give you missing output exceptions ([c200c06](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/c200c065c0e8dc2dec8bb065740dd798c42e76c6))
+* highlight model setup with best respective score(s) ([a31e600](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/a31e600ffafa25f053aab9b7510f7a8d65287273))
+* include new (and required) r-protoclust in treedist script dependencies ([6ea1cc6](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/6ea1cc6aeaced5ba491c6d82ae01f9a96f6e3961))
+* load protoclust in cluster_info_dist.R ([c606784](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/c6067847af0acc2dc2bba8d2cdb95cfcfbf422b4))
+* revert to working plot layout ([09aaf43](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/09aaf4378a8e11ad00eea8fb5e665880240aded1))
+* update names as needed ([27e4609](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/27e46094294c86612bd48cbc318e999b371579e4))
+* use extended regular expressions for sed extraction ([3a72bf7](https://www.github.com/hzi-bifo/phylogeny-of-single-cells/commit/3a72bf7316bdf93dd05c40618f52a13b53e652e2))