From 086cd15db7e400a95747a22b568a701691bb9027 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Wed, 14 Oct 2020 12:37:23 +0200 Subject: [PATCH 1/7] add `ete3 mod` to tests To check for https://github.com/etetoolkit/ete/issues/195 --- recipe/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipe/meta.yaml b/recipe/meta.yaml index e941885..12cbbe2 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -56,6 +56,7 @@ test: commands: - ete3 --help + - ete3 mod --help # ete3 cmdline tools not officially supported on win # https://groups.google.com/d/msg/etetoolkit/G3QmfxK1Vuk/txqlTTjLEAAJ - ete3 build check # [not win] From 6aa1d39d7167caf60129611fd7b3cd853e946235 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Wed, 14 Oct 2020 12:39:22 +0200 Subject: [PATCH 2/7] bump --- recipe/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipe/meta.yaml b/recipe/meta.yaml index 12cbbe2..f3bbcf5 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -14,7 +14,7 @@ source: build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --no-deps -vv entry_points: - ete3 = ete3.tools.ete:main From 360528d94163ead9dfda71f44172d6ff4293aaea Mon Sep 17 00:00:00 2001 From: conda-forge-linter Date: Wed, 14 Oct 2020 10:55:59 +0000 Subject: [PATCH 3/7] MNT: Re-rendered with conda-build 3.20.3, conda-smithy 3.8.2, and conda-forge-pinning 2020.10.13.19.09.25 --- .azure-pipelines/azure-pipelines-linux.yml | 1 - .scripts/build_steps.sh | 26 ++++++++++++++++------ .scripts/run_docker_build.sh | 2 ++ README.md | 6 +++-- build-locally.py | 12 ++++++++++ 5 files changed, 37 insertions(+), 10 deletions(-) diff --git a/.azure-pipelines/azure-pipelines-linux.yml b/.azure-pipelines/azure-pipelines-linux.yml index 89ab23f..b54e246 100755 --- a/.azure-pipelines/azure-pipelines-linux.yml +++ b/.azure-pipelines/azure-pipelines-linux.yml @@ -12,7 +12,6 @@ jobs: CONFIG: linux_64_ UPLOAD_PACKAGES: 'True' DOCKER_IMAGE: condaforge/linux-anvil-comp7 - maxParallel: 8 timeoutInMinutes: 360 steps: diff --git a/.scripts/build_steps.sh b/.scripts/build_steps.sh index 77fc067..63af1c6 100755 --- a/.scripts/build_steps.sh +++ b/.scripts/build_steps.sh @@ -19,7 +19,7 @@ conda-build: CONDARC -conda install --yes --quiet conda-forge-ci-setup=3 conda-build pip -c conda-forge +conda install --yes --quiet "conda-forge-ci-setup=3" conda-build pip -c conda-forge # set up the condarc setup_conda_rc "${FEEDSTOCK_ROOT}" "${RECIPE_ROOT}" "${CONFIG_FILE}" @@ -37,13 +37,25 @@ source run_conda_forge_build_setup # make the build number clobber make_build_number "${FEEDSTOCK_ROOT}" "${RECIPE_ROOT}" "${CONFIG_FILE}" -conda build "${RECIPE_ROOT}" -m "${CI_SUPPORT}/${CONFIG}.yaml" \ - --suppress-variables ${EXTRA_CB_OPTIONS:-} \ - --clobber-file "${CI_SUPPORT}/clobber_${CONFIG}.yaml" -validate_recipe_outputs "${FEEDSTOCK_NAME}" -if [[ "${UPLOAD_PACKAGES}" != "False" ]]; then - upload_package --validate --feedstock-name="${FEEDSTOCK_NAME}" "${FEEDSTOCK_ROOT}" "${RECIPE_ROOT}" "${CONFIG_FILE}" +if [[ "${BUILD_WITH_CONDA_DEBUG:-0}" == 1 ]]; then + if [[ "x${BUILD_OUTPUT_ID:-}" != "x" ]]; then + EXTRA_CB_OPTIONS="${EXTRA_CB_OPTIONS:-} --output-id ${BUILD_OUTPUT_ID}" + fi + conda debug "${RECIPE_ROOT}" -m "${CI_SUPPORT}/${CONFIG}.yaml" \ + ${EXTRA_CB_OPTIONS:-} \ + --clobber-file "${CI_SUPPORT}/clobber_${CONFIG}.yaml" + # Drop into an interactive shell + /bin/bash +else + conda build "${RECIPE_ROOT}" -m "${CI_SUPPORT}/${CONFIG}.yaml" \ + --suppress-variables ${EXTRA_CB_OPTIONS:-} \ + --clobber-file "${CI_SUPPORT}/clobber_${CONFIG}.yaml" + validate_recipe_outputs "${FEEDSTOCK_NAME}" + + if [[ "${UPLOAD_PACKAGES}" != "False" ]]; then + upload_package --validate --feedstock-name="${FEEDSTOCK_NAME}" "${FEEDSTOCK_ROOT}" "${RECIPE_ROOT}" "${CONFIG_FILE}" + fi fi touch "${FEEDSTOCK_ROOT}/build_artifacts/conda-forge-build-done-${CONFIG}" \ No newline at end of file diff --git a/.scripts/run_docker_build.sh b/.scripts/run_docker_build.sh index e4d5bab..87ba4db 100755 --- a/.scripts/run_docker_build.sh +++ b/.scripts/run_docker_build.sh @@ -74,6 +74,8 @@ docker run ${DOCKER_RUN_ARGS} \ -e CI \ -e FEEDSTOCK_NAME \ -e CPU_COUNT \ + -e BUILD_WITH_CONDA_DEBUG \ + -e BUILD_OUTPUT_ID \ -e BINSTAR_TOKEN \ -e FEEDSTOCK_TOKEN \ -e STAGING_BINSTAR_TOKEN \ diff --git a/README.md b/README.md index 39f2393..4c187b0 100644 --- a/README.md +++ b/README.md @@ -3,13 +3,15 @@ About ete3 Home: http://etetoolkit.org/ -Package license: GPLv3 +Package license: GPL-3.0-only -Feedstock license: BSD-3-Clause +Feedstock license: [BSD-3-Clause](https://github.com/conda-forge/ete3-feedstock/blob/master/LICENSE.txt) Summary: Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree. +Development: https://github.com/etetoolkit/ete +Documentation: http://etetoolkit.org/ Current build status ==================== diff --git a/build-locally.py b/build-locally.py index 8f7ecca..3453cfe 100755 --- a/build-locally.py +++ b/build-locally.py @@ -12,6 +12,10 @@ def setup_environment(ns): os.environ["CONFIG"] = ns.config os.environ["UPLOAD_PACKAGES"] = "False" + if ns.debug: + os.environ["BUILD_WITH_CONDA_DEBUG"] = "1" + if ns.output_id: + os.environ["BUILD_OUTPUT_ID"] = ns.output_id def run_docker_build(ns): @@ -51,6 +55,14 @@ def verify_config(ns): def main(args=None): p = ArgumentParser("build-locally") p.add_argument("config", default=None, nargs="?") + p.add_argument( + "--debug", + action="store_true", + help="Setup debug environment using `conda debug`", + ) + p.add_argument( + "--output-id", help="If running debug, specify the output to setup." + ) ns = p.parse_args(args=args) verify_config(ns) From 1b01661abfb83c56c6745aa8836f498f4ee9a80b Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Wed, 14 Oct 2020 13:27:51 +0200 Subject: [PATCH 4/7] import patch --- recipe/import.patch | 957 ++++++++++++++++++++++++++++++++++++++++++++ recipe/meta.yaml | 2 + 2 files changed, 959 insertions(+) create mode 100644 recipe/import.patch diff --git a/recipe/import.patch b/recipe/import.patch new file mode 100644 index 0000000..fe94e43 --- /dev/null +++ b/recipe/import.patch @@ -0,0 +1,957 @@ +diff -ruN /tmp/ete/.coveragerc /tmp/ete_new/.coveragerc +--- /tmp/ete/.coveragerc 2020-10-14 12:57:02.475810686 +0200 ++++ /tmp/ete_new/.coveragerc 1970-01-01 01:00:00.000000000 +0100 +@@ -1,24 +0,0 @@ +-[run] +-omit = +- */ete3/test/* +- +- # unmaintained +- */ete3/phylomedb/* +- +- # There are no GUI tests +- */ete3/treeview/qt4_gui.py +- */ete3/treeview/node_gui_actions.py +- */__init__.py +- +- +-source = ete3 +-branch = True +-include = */ete3/* +- +-[report] +-exclude_lines = +- pragma: no cover +- def __repr__ +- raise NotImplementedError +- if __name__ == .__main__.: +- +diff -ruN /tmp/ete/ete3/__init__.py /tmp/ete_new/ete3/__init__.py +--- /tmp/ete/ete3/__init__.py 2020-10-14 12:57:02.479810691 +0200 ++++ /tmp/ete_new/ete3/__init__.py 2020-10-14 13:22:02.901607573 +0200 +@@ -65,14 +65,10 @@ + except ImportError as e: + pass + +-try: +- from .treeview.svg_colors import * +- from .treeview.main import * +- from .treeview.faces import * +- from .treeview import faces +- from .treeview import layouts +-except ImportError as e: +- pass ++from .treeview.svg_colors import * ++from .treeview.main import * ++from .treeview.faces import * ++from .treeview import layouts + + try: + from .version import __version__ +diff -ruN /tmp/ete/.git/config /tmp/ete_new/.git/config +--- /tmp/ete/.git/config 2020-10-14 12:57:02.423810626 +0200 ++++ /tmp/ete_new/.git/config 1970-01-01 01:00:00.000000000 +0100 +@@ -1,11 +0,0 @@ +-[core] +- repositoryformatversion = 0 +- filemode = true +- bare = false +- logallrefupdates = true +-[remote "origin"] +- url = https://github.com/etetoolkit/ete.git +- fetch = +refs/heads/*:refs/remotes/origin/* +-[branch "master"] +- remote = origin +- merge = refs/heads/master +diff -ruN /tmp/ete/.git/description /tmp/ete_new/.git/description +--- /tmp/ete/.git/description 2020-10-14 12:56:56.863804220 +0200 ++++ /tmp/ete_new/.git/description 1970-01-01 01:00:00.000000000 +0100 +@@ -1 +0,0 @@ +-Unnamed repository; edit this file 'description' to name the repository. +diff -ruN /tmp/ete/.git/HEAD /tmp/ete_new/.git/HEAD +--- /tmp/ete/.git/HEAD 2020-10-14 12:57:02.419810621 +0200 ++++ /tmp/ete_new/.git/HEAD 1970-01-01 01:00:00.000000000 +0100 +@@ -1 +0,0 @@ +-ref: refs/heads/master +diff -ruN /tmp/ete/.git/hooks/applypatch-msg.sample /tmp/ete_new/.git/hooks/applypatch-msg.sample +--- /tmp/ete/.git/hooks/applypatch-msg.sample 2020-10-14 12:56:56.867804225 +0200 ++++ /tmp/ete_new/.git/hooks/applypatch-msg.sample 1970-01-01 01:00:00.000000000 +0100 +@@ -1,15 +0,0 @@ +-#!/bin/sh +-# +-# An example hook script to check the commit log message taken by +-# applypatch from an e-mail message. +-# +-# The hook should exit with non-zero status after issuing an +-# appropriate message if it wants to stop the commit. The hook is +-# allowed to edit the commit message file. +-# +-# To enable this hook, rename this file to "applypatch-msg". +- +-. git-sh-setup +-commitmsg="$(git rev-parse --git-path hooks/commit-msg)" +-test -x "$commitmsg" && exec "$commitmsg" ${1+"$@"} +-: +diff -ruN /tmp/ete/.git/hooks/commit-msg.sample /tmp/ete_new/.git/hooks/commit-msg.sample +--- /tmp/ete/.git/hooks/commit-msg.sample 2020-10-14 12:56:56.863804220 +0200 ++++ /tmp/ete_new/.git/hooks/commit-msg.sample 1970-01-01 01:00:00.000000000 +0100 +@@ -1,24 +0,0 @@ +-#!/bin/sh +-# +-# An example hook script to check the commit log message. +-# Called by "git commit" with one argument, the name of the file +-# that has the commit message. The hook should exit with non-zero +-# status after issuing an appropriate message if it wants to stop the +-# commit. The hook is allowed to edit the commit message file. +-# +-# To enable this hook, rename this file to "commit-msg". +- +-# Uncomment the below to add a Signed-off-by line to the message. +-# Doing this in a hook is a bad idea in general, but the prepare-commit-msg +-# hook is more suited to it. +-# +-# SOB=$(git var GIT_AUTHOR_IDENT | sed -n 's/^\(.*>\).*$/Signed-off-by: \1/p') +-# grep -qs "^$SOB" "$1" || echo "$SOB" >> "$1" +- +-# This example catches duplicate Signed-off-by lines. +- +-test "" = "$(grep '^Signed-off-by: ' "$1" | +- sort | uniq -c | sed -e '/^[ ]*1[ ]/d')" || { +- echo >&2 Duplicate Signed-off-by lines. +- exit 1 +-} +diff -ruN /tmp/ete/.git/hooks/fsmonitor-watchman.sample /tmp/ete_new/.git/hooks/fsmonitor-watchman.sample +--- /tmp/ete/.git/hooks/fsmonitor-watchman.sample 2020-10-14 12:56:56.863804220 +0200 ++++ /tmp/ete_new/.git/hooks/fsmonitor-watchman.sample 1970-01-01 01:00:00.000000000 +0100 +@@ -1,114 +0,0 @@ +-#!/usr/bin/perl +- +-use strict; +-use warnings; +-use IPC::Open2; +- +-# An example hook script to integrate Watchman +-# (https://facebook.github.io/watchman/) with git to speed up detecting +-# new and modified files. +-# +-# The hook is passed a version (currently 1) and a time in nanoseconds +-# formatted as a string and outputs to stdout all files that have been +-# modified since the given time. Paths must be relative to the root of +-# the working tree and separated by a single NUL. +-# +-# To enable this hook, rename this file to "query-watchman" and set +-# 'git config core.fsmonitor .git/hooks/query-watchman' +-# +-my ($version, $time) = @ARGV; +- +-# Check the hook interface version +- +-if ($version == 1) { +- # convert nanoseconds to seconds +- $time = int $time / 1000000000; +-} else { +- die "Unsupported query-fsmonitor hook version '$version'.\n" . +- "Falling back to scanning...\n"; +-} +- +-my $git_work_tree; +-if ($^O =~ 'msys' || $^O =~ 'cygwin') { +- $git_work_tree = Win32::GetCwd(); +- $git_work_tree =~ tr/\\/\//; +-} else { +- require Cwd; +- $git_work_tree = Cwd::cwd(); +-} +- +-my $retry = 1; +- +-launch_watchman(); +- +-sub launch_watchman { +- +- my $pid = open2(\*CHLD_OUT, \*CHLD_IN, 'watchman -j --no-pretty') +- or die "open2() failed: $!\n" . +- "Falling back to scanning...\n"; +- +- # In the query expression below we're asking for names of files that +- # changed since $time but were not transient (ie created after +- # $time but no longer exist). +- # +- # To accomplish this, we're using the "since" generator to use the +- # recency index to select candidate nodes and "fields" to limit the +- # output to file names only. Then we're using the "expression" term to +- # further constrain the results. +- # +- # The category of transient files that we want to ignore will have a +- # creation clock (cclock) newer than $time_t value and will also not +- # currently exist. +- +- my $query = <<" END"; +- ["query", "$git_work_tree", { +- "since": $time, +- "fields": ["name"], +- "expression": ["not", ["allof", ["since", $time, "cclock"], ["not", "exists"]]] +- }] +- END +- +- print CHLD_IN $query; +- close CHLD_IN; +- my $response = do {local $/; }; +- +- die "Watchman: command returned no output.\n" . +- "Falling back to scanning...\n" if $response eq ""; +- die "Watchman: command returned invalid output: $response\n" . +- "Falling back to scanning...\n" unless $response =~ /^\{/; +- +- my $json_pkg; +- eval { +- require JSON::XS; +- $json_pkg = "JSON::XS"; +- 1; +- } or do { +- require JSON::PP; +- $json_pkg = "JSON::PP"; +- }; +- +- my $o = $json_pkg->new->utf8->decode($response); +- +- if ($retry > 0 and $o->{error} and $o->{error} =~ m/unable to resolve root .* directory (.*) is not watched/) { +- print STDERR "Adding '$git_work_tree' to watchman's watch list.\n"; +- $retry--; +- qx/watchman watch "$git_work_tree"/; +- die "Failed to make watchman watch '$git_work_tree'.\n" . +- "Falling back to scanning...\n" if $? != 0; +- +- # Watchman will always return all files on the first query so +- # return the fast "everything is dirty" flag to git and do the +- # Watchman query just to get it over with now so we won't pay +- # the cost in git to look up each individual file. +- print "/\0"; +- eval { launch_watchman() }; +- exit 0; +- } +- +- die "Watchman: $o->{error}.\n" . +- "Falling back to scanning...\n" if $o->{error}; +- +- binmode STDOUT, ":utf8"; +- local $, = "\0"; +- print @{$o->{files}}; +-} +diff -ruN /tmp/ete/.git/hooks/post-update.sample /tmp/ete_new/.git/hooks/post-update.sample +--- /tmp/ete/.git/hooks/post-update.sample 2020-10-14 12:56:56.867804225 +0200 ++++ /tmp/ete_new/.git/hooks/post-update.sample 1970-01-01 01:00:00.000000000 +0100 +@@ -1,8 +0,0 @@ +-#!/bin/sh +-# +-# An example hook script to prepare a packed repository for use over +-# dumb transports. +-# +-# To enable this hook, rename this file to "post-update". +- +-exec git update-server-info +diff -ruN /tmp/ete/.git/hooks/pre-applypatch.sample /tmp/ete_new/.git/hooks/pre-applypatch.sample +--- /tmp/ete/.git/hooks/pre-applypatch.sample 2020-10-14 12:56:56.863804220 +0200 ++++ /tmp/ete_new/.git/hooks/pre-applypatch.sample 1970-01-01 01:00:00.000000000 +0100 +@@ -1,14 +0,0 @@ +-#!/bin/sh +-# +-# An example hook script to verify what is about to be committed +-# by applypatch from an e-mail message. +-# +-# The hook should exit with non-zero status after issuing an +-# appropriate message if it wants to stop the commit. +-# +-# To enable this hook, rename this file to "pre-applypatch". +- +-. git-sh-setup +-precommit="$(git rev-parse --git-path hooks/pre-commit)" +-test -x "$precommit" && exec "$precommit" ${1+"$@"} +-: +diff -ruN /tmp/ete/.git/hooks/pre-commit.sample /tmp/ete_new/.git/hooks/pre-commit.sample +--- /tmp/ete/.git/hooks/pre-commit.sample 2020-10-14 12:56:56.867804225 +0200 ++++ /tmp/ete_new/.git/hooks/pre-commit.sample 1970-01-01 01:00:00.000000000 +0100 +@@ -1,49 +0,0 @@ +-#!/bin/sh +-# +-# An example hook script to verify what is about to be committed. +-# Called by "git commit" with no arguments. The hook should +-# exit with non-zero status after issuing an appropriate message if +-# it wants to stop the commit. +-# +-# To enable this hook, rename this file to "pre-commit". +- +-if git rev-parse --verify HEAD >/dev/null 2>&1 +-then +- against=HEAD +-else +- # Initial commit: diff against an empty tree object +- against=4b825dc642cb6eb9a060e54bf8d69288fbee4904 +-fi +- +-# If you want to allow non-ASCII filenames set this variable to true. +-allownonascii=$(git config --bool hooks.allownonascii) +- +-# Redirect output to stderr. +-exec 1>&2 +- +-# Cross platform projects tend to avoid non-ASCII filenames; prevent +-# them from being added to the repository. We exploit the fact that the +-# printable range starts at the space character and ends with tilde. +-if [ "$allownonascii" != "true" ] && +- # Note that the use of brackets around a tr range is ok here, (it's +- # even required, for portability to Solaris 10's /usr/bin/tr), since +- # the square bracket bytes happen to fall in the designated range. +- test $(git diff --cached --name-only --diff-filter=A -z $against | +- LC_ALL=C tr -d '[ -~]\0' | wc -c) != 0 +-then +- cat <<\EOF +-Error: Attempt to add a non-ASCII file name. +- +-This can cause problems if you want to work with people on other platforms. +- +-To be portable it is advisable to rename the file. +- +-If you know what you are doing you can disable this check using: +- +- git config hooks.allownonascii true +-EOF +- exit 1 +-fi +- +-# If there are whitespace errors, print the offending file names and fail. +-exec git diff-index --check --cached $against -- +diff -ruN /tmp/ete/.git/hooks/prepare-commit-msg.sample /tmp/ete_new/.git/hooks/prepare-commit-msg.sample +--- /tmp/ete/.git/hooks/prepare-commit-msg.sample 2020-10-14 12:56:56.863804220 +0200 ++++ /tmp/ete_new/.git/hooks/prepare-commit-msg.sample 1970-01-01 01:00:00.000000000 +0100 +@@ -1,42 +0,0 @@ +-#!/bin/sh +-# +-# An example hook script to prepare the commit log message. +-# Called by "git commit" with the name of the file that has the +-# commit message, followed by the description of the commit +-# message's source. The hook's purpose is to edit the commit +-# message file. If the hook fails with a non-zero status, +-# the commit is aborted. +-# +-# To enable this hook, rename this file to "prepare-commit-msg". +- +-# This hook includes three examples. The first one removes the +-# "# Please enter the commit message..." help message. +-# +-# The second includes the output of "git diff --name-status -r" +-# into the message, just before the "git status" output. It is +-# commented because it doesn't cope with --amend or with squashed +-# commits. +-# +-# The third example adds a Signed-off-by line to the message, that can +-# still be edited. This is rarely a good idea. +- +-COMMIT_MSG_FILE=$1 +-COMMIT_SOURCE=$2 +-SHA1=$3 +- +-/usr/bin/perl -i.bak -ne 'print unless(m/^. Please enter the commit message/..m/^#$/)' "$COMMIT_MSG_FILE" +- +-# case "$COMMIT_SOURCE,$SHA1" in +-# ,|template,) +-# /usr/bin/perl -i.bak -pe ' +-# print "\n" . `git diff --cached --name-status -r` +-# if /^#/ && $first++ == 0' "$COMMIT_MSG_FILE" ;; +-# *) ;; +-# esac +- +-# SOB=$(git var GIT_COMMITTER_IDENT | sed -n 's/^\(.*>\).*$/Signed-off-by: \1/p') +-# git interpret-trailers --in-place --trailer "$SOB" "$COMMIT_MSG_FILE" +-# if test -z "$COMMIT_SOURCE" +-# then +-# /usr/bin/perl -i.bak -pe 'print "\n" if !$first_line++' "$COMMIT_MSG_FILE" +-# fi +diff -ruN /tmp/ete/.git/hooks/pre-push.sample /tmp/ete_new/.git/hooks/pre-push.sample +--- /tmp/ete/.git/hooks/pre-push.sample 2020-10-14 12:56:56.863804220 +0200 ++++ /tmp/ete_new/.git/hooks/pre-push.sample 1970-01-01 01:00:00.000000000 +0100 +@@ -1,53 +0,0 @@ +-#!/bin/sh +- +-# An example hook script to verify what is about to be pushed. Called by "git +-# push" after it has checked the remote status, but before anything has been +-# pushed. If this script exits with a non-zero status nothing will be pushed. +-# +-# This hook is called with the following parameters: +-# +-# $1 -- Name of the remote to which the push is being done +-# $2 -- URL to which the push is being done +-# +-# If pushing without using a named remote those arguments will be equal. +-# +-# Information about the commits which are being pushed is supplied as lines to +-# the standard input in the form: +-# +-# +-# +-# This sample shows how to prevent push of commits where the log message starts +-# with "WIP" (work in progress). +- +-remote="$1" +-url="$2" +- +-z40=0000000000000000000000000000000000000000 +- +-while read local_ref local_sha remote_ref remote_sha +-do +- if [ "$local_sha" = $z40 ] +- then +- # Handle delete +- : +- else +- if [ "$remote_sha" = $z40 ] +- then +- # New branch, examine all commits +- range="$local_sha" +- else +- # Update to existing branch, examine new commits +- range="$remote_sha..$local_sha" +- fi +- +- # Check for WIP commit +- commit=`git rev-list -n 1 --grep '^WIP' "$range"` +- if [ -n "$commit" ] +- then +- echo >&2 "Found WIP commit in $local_ref, not pushing" +- exit 1 +- fi +- fi +-done +- +-exit 0 +diff -ruN /tmp/ete/.git/hooks/pre-rebase.sample /tmp/ete_new/.git/hooks/pre-rebase.sample +--- /tmp/ete/.git/hooks/pre-rebase.sample 2020-10-14 12:56:56.863804220 +0200 ++++ /tmp/ete_new/.git/hooks/pre-rebase.sample 1970-01-01 01:00:00.000000000 +0100 +@@ -1,169 +0,0 @@ +-#!/bin/sh +-# +-# Copyright (c) 2006, 2008 Junio C Hamano +-# +-# The "pre-rebase" hook is run just before "git rebase" starts doing +-# its job, and can prevent the command from running by exiting with +-# non-zero status. +-# +-# The hook is called with the following parameters: +-# +-# $1 -- the upstream the series was forked from. +-# $2 -- the branch being rebased (or empty when rebasing the current branch). +-# +-# This sample shows how to prevent topic branches that are already +-# merged to 'next' branch from getting rebased, because allowing it +-# would result in rebasing already published history. +- +-publish=next +-basebranch="$1" +-if test "$#" = 2 +-then +- topic="refs/heads/$2" +-else +- topic=`git symbolic-ref HEAD` || +- exit 0 ;# we do not interrupt rebasing detached HEAD +-fi +- +-case "$topic" in +-refs/heads/??/*) +- ;; +-*) +- exit 0 ;# we do not interrupt others. +- ;; +-esac +- +-# Now we are dealing with a topic branch being rebased +-# on top of master. Is it OK to rebase it? +- +-# Does the topic really exist? +-git show-ref -q "$topic" || { +- echo >&2 "No such branch $topic" +- exit 1 +-} +- +-# Is topic fully merged to master? +-not_in_master=`git rev-list --pretty=oneline ^master "$topic"` +-if test -z "$not_in_master" +-then +- echo >&2 "$topic is fully merged to master; better remove it." +- exit 1 ;# we could allow it, but there is no point. +-fi +- +-# Is topic ever merged to next? If so you should not be rebasing it. +-only_next_1=`git rev-list ^master "^$topic" ${publish} | sort` +-only_next_2=`git rev-list ^master ${publish} | sort` +-if test "$only_next_1" = "$only_next_2" +-then +- not_in_topic=`git rev-list "^$topic" master` +- if test -z "$not_in_topic" +- then +- echo >&2 "$topic is already up to date with master" +- exit 1 ;# we could allow it, but there is no point. +- else +- exit 0 +- fi +-else +- not_in_next=`git rev-list --pretty=oneline ^${publish} "$topic"` +- /usr/bin/perl -e ' +- my $topic = $ARGV[0]; +- my $msg = "* $topic has commits already merged to public branch:\n"; +- my (%not_in_next) = map { +- /^([0-9a-f]+) /; +- ($1 => 1); +- } split(/\n/, $ARGV[1]); +- for my $elem (map { +- /^([0-9a-f]+) (.*)$/; +- [$1 => $2]; +- } split(/\n/, $ARGV[2])) { +- if (!exists $not_in_next{$elem->[0]}) { +- if ($msg) { +- print STDERR $msg; +- undef $msg; +- } +- print STDERR " $elem->[1]\n"; +- } +- } +- ' "$topic" "$not_in_next" "$not_in_master" +- exit 1 +-fi +- +-<<\DOC_END +- +-This sample hook safeguards topic branches that have been +-published from being rewound. +- +-The workflow assumed here is: +- +- * Once a topic branch forks from "master", "master" is never +- merged into it again (either directly or indirectly). +- +- * Once a topic branch is fully cooked and merged into "master", +- it is deleted. If you need to build on top of it to correct +- earlier mistakes, a new topic branch is created by forking at +- the tip of the "master". This is not strictly necessary, but +- it makes it easier to keep your history simple. +- +- * Whenever you need to test or publish your changes to topic +- branches, merge them into "next" branch. +- +-The script, being an example, hardcodes the publish branch name +-to be "next", but it is trivial to make it configurable via +-$GIT_DIR/config mechanism. +- +-With this workflow, you would want to know: +- +-(1) ... if a topic branch has ever been merged to "next". Young +- topic branches can have stupid mistakes you would rather +- clean up before publishing, and things that have not been +- merged into other branches can be easily rebased without +- affecting other people. But once it is published, you would +- not want to rewind it. +- +-(2) ... if a topic branch has been fully merged to "master". +- Then you can delete it. More importantly, you should not +- build on top of it -- other people may already want to +- change things related to the topic as patches against your +- "master", so if you need further changes, it is better to +- fork the topic (perhaps with the same name) afresh from the +- tip of "master". +- +-Let's look at this example: +- +- o---o---o---o---o---o---o---o---o---o "next" +- / / / / +- / a---a---b A / / +- / / / / +- / / c---c---c---c B / +- / / / \ / +- / / / b---b C \ / +- / / / / \ / +- ---o---o---o---o---o---o---o---o---o---o---o "master" +- +- +-A, B and C are topic branches. +- +- * A has one fix since it was merged up to "next". +- +- * B has finished. It has been fully merged up to "master" and "next", +- and is ready to be deleted. +- +- * C has not merged to "next" at all. +- +-We would want to allow C to be rebased, refuse A, and encourage +-B to be deleted. +- +-To compute (1): +- +- git rev-list ^master ^topic next +- git rev-list ^master next +- +- if these match, topic has not merged in next at all. +- +-To compute (2): +- +- git rev-list master..topic +- +- if this is empty, it is fully merged to "master". +- +-DOC_END +diff -ruN /tmp/ete/.git/hooks/pre-receive.sample /tmp/ete_new/.git/hooks/pre-receive.sample +--- /tmp/ete/.git/hooks/pre-receive.sample 2020-10-14 12:56:56.863804220 +0200 ++++ /tmp/ete_new/.git/hooks/pre-receive.sample 1970-01-01 01:00:00.000000000 +0100 +@@ -1,24 +0,0 @@ +-#!/bin/sh +-# +-# An example hook script to make use of push options. +-# The example simply echoes all push options that start with 'echoback=' +-# and rejects all pushes when the "reject" push option is used. +-# +-# To enable this hook, rename this file to "pre-receive". +- +-if test -n "$GIT_PUSH_OPTION_COUNT" +-then +- i=0 +- while test "$i" -lt "$GIT_PUSH_OPTION_COUNT" +- do +- eval "value=\$GIT_PUSH_OPTION_$i" +- case "$value" in +- echoback=*) +- echo "echo from the pre-receive-hook: ${value#*=}" >&2 +- ;; +- reject) +- exit 1 +- esac +- i=$((i + 1)) +- done +-fi +diff -ruN /tmp/ete/.git/hooks/update.sample /tmp/ete_new/.git/hooks/update.sample +--- /tmp/ete/.git/hooks/update.sample 2020-10-14 12:56:56.867804225 +0200 ++++ /tmp/ete_new/.git/hooks/update.sample 1970-01-01 01:00:00.000000000 +0100 +@@ -1,128 +0,0 @@ +-#!/bin/sh +-# +-# An example hook script to block unannotated tags from entering. +-# Called by "git receive-pack" with arguments: refname sha1-old sha1-new +-# +-# To enable this hook, rename this file to "update". +-# +-# Config +-# ------ +-# hooks.allowunannotated +-# This boolean sets whether unannotated tags will be allowed into the +-# repository. By default they won't be. +-# hooks.allowdeletetag +-# This boolean sets whether deleting tags will be allowed in the +-# repository. By default they won't be. +-# hooks.allowmodifytag +-# This boolean sets whether a tag may be modified after creation. By default +-# it won't be. +-# hooks.allowdeletebranch +-# This boolean sets whether deleting branches will be allowed in the +-# repository. By default they won't be. +-# hooks.denycreatebranch +-# This boolean sets whether remotely creating branches will be denied +-# in the repository. By default this is allowed. +-# +- +-# --- Command line +-refname="$1" +-oldrev="$2" +-newrev="$3" +- +-# --- Safety check +-if [ -z "$GIT_DIR" ]; then +- echo "Don't run this script from the command line." >&2 +- echo " (if you want, you could supply GIT_DIR then run" >&2 +- echo " $0 )" >&2 +- exit 1 +-fi +- +-if [ -z "$refname" -o -z "$oldrev" -o -z "$newrev" ]; then +- echo "usage: $0 " >&2 +- exit 1 +-fi +- +-# --- Config +-allowunannotated=$(git config --bool hooks.allowunannotated) +-allowdeletebranch=$(git config --bool hooks.allowdeletebranch) +-denycreatebranch=$(git config --bool hooks.denycreatebranch) +-allowdeletetag=$(git config --bool hooks.allowdeletetag) +-allowmodifytag=$(git config --bool hooks.allowmodifytag) +- +-# check for no description +-projectdesc=$(sed -e '1q' "$GIT_DIR/description") +-case "$projectdesc" in +-"Unnamed repository"* | "") +- echo "*** Project description file hasn't been set" >&2 +- exit 1 +- ;; +-esac +- +-# --- Check types +-# if $newrev is 0000...0000, it's a commit to delete a ref. +-zero="0000000000000000000000000000000000000000" +-if [ "$newrev" = "$zero" ]; then +- newrev_type=delete +-else +- newrev_type=$(git cat-file -t $newrev) +-fi +- +-case "$refname","$newrev_type" in +- refs/tags/*,commit) +- # un-annotated tag +- short_refname=${refname##refs/tags/} +- if [ "$allowunannotated" != "true" ]; then +- echo "*** The un-annotated tag, $short_refname, is not allowed in this repository" >&2 +- echo "*** Use 'git tag [ -a | -s ]' for tags you want to propagate." >&2 +- exit 1 +- fi +- ;; +- refs/tags/*,delete) +- # delete tag +- if [ "$allowdeletetag" != "true" ]; then +- echo "*** Deleting a tag is not allowed in this repository" >&2 +- exit 1 +- fi +- ;; +- refs/tags/*,tag) +- # annotated tag +- if [ "$allowmodifytag" != "true" ] && git rev-parse $refname > /dev/null 2>&1 +- then +- echo "*** Tag '$refname' already exists." >&2 +- echo "*** Modifying a tag is not allowed in this repository." >&2 +- exit 1 +- fi +- ;; +- refs/heads/*,commit) +- # branch +- if [ "$oldrev" = "$zero" -a "$denycreatebranch" = "true" ]; then +- echo "*** Creating a branch is not allowed in this repository" >&2 +- exit 1 +- fi +- ;; +- refs/heads/*,delete) +- # delete branch +- if [ "$allowdeletebranch" != "true" ]; then +- echo "*** Deleting a branch is not allowed in this repository" >&2 +- exit 1 +- fi +- ;; +- refs/remotes/*,commit) +- # tracking branch +- ;; +- refs/remotes/*,delete) +- # delete tracking branch +- if [ "$allowdeletebranch" != "true" ]; then +- echo "*** Deleting a tracking branch is not allowed in this repository" >&2 +- exit 1 +- fi +- ;; +- *) +- # Anything else (is there anything else?) +- echo "*** Update hook: unknown type of update to ref $refname of type $newrev_type" >&2 +- exit 1 +- ;; +-esac +- +-# --- Finished +-exit 0 +Binary files /tmp/ete/.git/index and /tmp/ete_new/.git/index differ +diff -ruN /tmp/ete/.git/info/exclude /tmp/ete_new/.git/info/exclude +--- /tmp/ete/.git/info/exclude 2020-10-14 12:56:56.859804216 +0200 ++++ /tmp/ete_new/.git/info/exclude 1970-01-01 01:00:00.000000000 +0100 +@@ -1,6 +0,0 @@ +-# git ls-files --others --exclude-from=.git/info/exclude +-# Lines that start with '#' are comments. +-# For a project mostly in C, the following would be a good set of +-# exclude patterns (uncomment them if you want to use them): +-# *.[oa] +-# *~ +diff -ruN /tmp/ete/.git/logs/HEAD /tmp/ete_new/.git/logs/HEAD +--- /tmp/ete/.git/logs/HEAD 2020-10-14 12:57:02.419810621 +0200 ++++ /tmp/ete_new/.git/logs/HEAD 1970-01-01 01:00:00.000000000 +0100 +@@ -1 +0,0 @@ +-0000000000000000000000000000000000000000 97e0ce9fab2f2286c69fb31577df75684613e769 Matthias Bernt 1602673022 +0200 clone: from https://github.com/etetoolkit/ete.git +diff -ruN /tmp/ete/.git/logs/refs/heads/master /tmp/ete_new/.git/logs/refs/heads/master +--- /tmp/ete/.git/logs/refs/heads/master 2020-10-14 12:57:02.419810621 +0200 ++++ /tmp/ete_new/.git/logs/refs/heads/master 1970-01-01 01:00:00.000000000 +0100 +@@ -1 +0,0 @@ +-0000000000000000000000000000000000000000 97e0ce9fab2f2286c69fb31577df75684613e769 Matthias Bernt 1602673022 +0200 clone: from https://github.com/etetoolkit/ete.git +diff -ruN /tmp/ete/.git/logs/refs/remotes/origin/HEAD /tmp/ete_new/.git/logs/refs/remotes/origin/HEAD +--- /tmp/ete/.git/logs/refs/remotes/origin/HEAD 2020-10-14 12:57:02.419810621 +0200 ++++ /tmp/ete_new/.git/logs/refs/remotes/origin/HEAD 1970-01-01 01:00:00.000000000 +0100 +@@ -1 +0,0 @@ +-0000000000000000000000000000000000000000 97e0ce9fab2f2286c69fb31577df75684613e769 Matthias Bernt 1602673022 +0200 clone: from https://github.com/etetoolkit/ete.git +Binary files /tmp/ete/.git/objects/pack/pack-10afe30094a02542c4e9929d1213732e6d8cb147.idx and /tmp/ete_new/.git/objects/pack/pack-10afe30094a02542c4e9929d1213732e6d8cb147.idx differ +Binary files /tmp/ete/.git/objects/pack/pack-10afe30094a02542c4e9929d1213732e6d8cb147.pack and /tmp/ete_new/.git/objects/pack/pack-10afe30094a02542c4e9929d1213732e6d8cb147.pack differ +diff -ruN /tmp/ete/.git/packed-refs /tmp/ete_new/.git/packed-refs +--- /tmp/ete/.git/packed-refs 2020-10-14 12:57:02.419810621 +0200 ++++ /tmp/ete_new/.git/packed-refs 1970-01-01 01:00:00.000000000 +0100 +@@ -1,64 +0,0 @@ +-# pack-refs with: peeled fully-peeled sorted +-4a59044e8ea7d3389beb430a52329b5a15836fd2 refs/remotes/origin/2.1 +-cba7dc2560dff85be068c51d6c0ac676ec36b203 refs/remotes/origin/2.2 +-1674999f39cca8621886ac9a2aa74df80072014d refs/remotes/origin/2.3 +-b54e5706815edb40cc25deb2be9b1e8865ccc824 refs/remotes/origin/3.0 +-3c4321c4eb2f754fe15aef9b7d137f48e7d98202 refs/remotes/origin/e5_tweaks +-c3aadbc3feb64c5f88f174b6c37ebd949942c9b3 refs/remotes/origin/feature/iqtree +-97e0ce9fab2f2286c69fb31577df75684613e769 refs/remotes/origin/master +-59dea1b7218829757f32c58934e292d6158a9948 refs/remotes/origin/mca_method_issue_398 +-1dd23f9701577142eaa4a5793fd58c2aadc1387b refs/remotes/origin/ncbi +-0d37affe2745eed37a8333e4c5c998c7832fee1b refs/remotes/origin/qt5 +-4358351578f924c87d1c4c02498ca1abc636bd31 refs/remotes/origin/revert-405-master +-8fad9ca30d2957b8f6af33957c1cc9f1d85353f5 refs/tags/2.3.0-rc1 +-7b67b6f10abfdf404f3d6d25235b5fcdecd28a70 refs/tags/2.3.0-rc2 +-c8d69050c3c63a23e9d9828b8e54501707964358 refs/tags/2.3.1 +-476722ec18338eb46037b06334e3b16c81bface2 refs/tags/2.3.10 +-14b1d6e7a0c77cbaca026ad5cf53d9c86f4a5bf4 refs/tags/2.3.2 +-e64d6ba3ae116ab766a599cc196935002e8eee19 refs/tags/2.3.3 +-007ae665bc24c76bd09b5e661b4c7e82bc4c36cc refs/tags/2.3.4 +-673a0eefd0e838860d18e859adf32b564023f712 refs/tags/2.3.5 +-f899dc56f2d09469ef03c61dfb0d4e955aa76e36 refs/tags/2.3.6 +-a3b4d7b44f3e8fa541f4e6c5b6e87e45ff5e46c8 refs/tags/2.3.7 +-7dd6d48b12ea48228cb6e8dd8f81536d094e70b5 refs/tags/2.3.8 +-85055442da7eae443b0247e2363c7ac3b8b36f44 refs/tags/2.3.9 +-4d18e36242e0ce95e549b3906d1251a101f9583a refs/tags/3.0.0-b5 +-3a5759ce7f48bdd3f9236a2df710aeef6e169207 refs/tags/3.0.0-beta2 +-265ce76c7b59d89fe0375f43e6e237804fe0e40e refs/tags/3.0.0-beta3 +-a62bb582c727c896ebe7680f37641f30dd0f0547 refs/tags/3.0.0-beta4 +-9b8f746b2888e54f82a41a2f4b51107a59d54520 refs/tags/3.0.0b10 +-dec013b5f13c2842acc2d8961b1f39031dc8dc61 refs/tags/3.0.0b11 +-6027a62486670343b9466c74fdfe9e5dc64d4b10 refs/tags/3.0.0b12 +-0f7be592f13bca0692f1aee356481a915296c73b refs/tags/3.0.0b13 +-f33b23acaeebd1fbce4830ad4a6c40d4cd82212c refs/tags/3.0.0b14 +-675c5f90ff18811ad65aeb2ab8231bba54f1c5b0 refs/tags/3.0.0b15 +-8007cd6575d34daa1804161aaee66c66b847c594 refs/tags/3.0.0b16 +-db605af689562c06e29a975453f35d2fc2bf0ed6 refs/tags/3.0.0b17 +-ccb825a4bd9ce4042eff9e3b6d8bfca81207203c refs/tags/3.0.0b18 +-21281d17324517921f2b8a73f444cae3392053cf refs/tags/3.0.0b19 +-c728ec534f8277ecf8bf03e41e7e3eacaeb7054a refs/tags/3.0.0b20 +-69a8f9012641064e2d435ee577ac33f6b11f93e1 refs/tags/3.0.0b21 +-e1323ee079ada8fd4c373fb007f6affc16578221 refs/tags/3.0.0b22 +-b445737f33f42863dbd238dadb1f3da8f36abde3 refs/tags/3.0.0b23 +-57ab6dc46044a2810f0d2347403817436f45a3c8 refs/tags/3.0.0b24 +-b1e5d29c0326adef7d1a851d2a24f859ff3a01b9 refs/tags/3.0.0b25 +-b4e0eb2dedaecdc4550df830b82ca6df9341a1c6 refs/tags/3.0.0b26 +-c267c07531f3e17884eb4568ddc9755e436d1224 refs/tags/3.0.0b27 +-e9b37f45df6059072e4daed567036d32f0b85df8 refs/tags/3.0.0b28 +-671e6bba533631e6544da8dce269589de96f9d96 refs/tags/3.0.0b29 +-7ff437c3b6939a1c56c6a95e524522f57b663383 refs/tags/3.0.0b30 +-fe1b799b7f1def070435a4b506c688b027e7e7cf refs/tags/3.0.0b31 +-2f4ea9d293ff616ffd9dd446437425c59d3963db refs/tags/3.0.0b32 +-0d9ff08b577c1992aa3594413368a13eeada9641 refs/tags/3.0.0b33 +-4dca7aa430715e0d653116d7fc4a2e1a5ee8ff75 refs/tags/3.0.0b34 +-a734959f8ed5667c0cfb1713c9a2cd321ae0eb05 refs/tags/3.0.0b35 +-b54e5706815edb40cc25deb2be9b1e8865ccc824 refs/tags/3.0.0b36 +-1d764af9e80d91d67563d2e9a437462efee61505 refs/tags/3.0.0b6 +-48df4c5b25bdb43bad0a6894089e10cdd51eeab2 refs/tags/3.0.0b7 +-15160be480d0a47cac06dba30aee03ee16fc0226 refs/tags/3.0.0b8 +-139914f9565b63d19801ba7a183384d1aa7598b9 refs/tags/3.0.0b9 +-76f6cd12b5d6f113b76ef35bd95d9eb9a993d9f8 refs/tags/3.1.0 +-61e0390b437103e04ae338a28fec547adf73fd6b refs/tags/3.1.1 +-97e0ce9fab2f2286c69fb31577df75684613e769 refs/tags/3.1.2 +-4a59044e8ea7d3389beb430a52329b5a15836fd2 refs/tags/v2.1 +-cba7dc2560dff85be068c51d6c0ac676ec36b203 refs/tags/v2.2 +diff -ruN /tmp/ete/.git/refs/heads/master /tmp/ete_new/.git/refs/heads/master +--- /tmp/ete/.git/refs/heads/master 2020-10-14 12:57:02.419810621 +0200 ++++ /tmp/ete_new/.git/refs/heads/master 1970-01-01 01:00:00.000000000 +0100 +@@ -1 +0,0 @@ +-97e0ce9fab2f2286c69fb31577df75684613e769 +diff -ruN /tmp/ete/.git/refs/remotes/origin/HEAD /tmp/ete_new/.git/refs/remotes/origin/HEAD +--- /tmp/ete/.git/refs/remotes/origin/HEAD 2020-10-14 12:57:02.419810621 +0200 ++++ /tmp/ete_new/.git/refs/remotes/origin/HEAD 1970-01-01 01:00:00.000000000 +0100 +@@ -1 +0,0 @@ +-ref: refs/remotes/origin/master +diff -ruN /tmp/ete/.github/FUNDING.yml /tmp/ete_new/.github/FUNDING.yml +--- /tmp/ete/.github/FUNDING.yml 2020-10-14 12:57:02.475810686 +0200 ++++ /tmp/ete_new/.github/FUNDING.yml 1970-01-01 01:00:00.000000000 +0100 +@@ -1,12 +0,0 @@ +-# These are supported funding model platforms +- +-github: [jhcepas] +-patreon: # Replace with a single Patreon username +-open_collective: # Replace with a single Open Collective username +-ko_fi: # Replace with a single Ko-fi username +-tidelift: # Replace with a single Tidelift platform-name/package-name e.g., npm/babel +-community_bridge: # Replace with a single Community Bridge project-name e.g., cloud-foundry +-liberapay: # Replace with a single Liberapay username +-issuehunt: # Replace with a single IssueHunt username +-otechie: # Replace with a single Otechie username +-custom: # Replace with up to 4 custom sponsorship URLs e.g., ['link1', 'link2'] +diff -ruN /tmp/ete/.gitignore /tmp/ete_new/.gitignore +--- /tmp/ete/.gitignore 2020-10-14 12:57:02.475810686 +0200 ++++ /tmp/ete_new/.gitignore 1970-01-01 01:00:00.000000000 +0100 +@@ -1,25 +0,0 @@ +-build +-*.pyc +-*~ +-#*# +-doc/_build/ +-dist/ +-*.egg-info +- +-# Conda testing environment +-miniconda.sh +-miniconda/ +- +-# Test files +-tests.log +-test.png +-test.pdf +-test.svg +-testdb.sqlite* +-ete_test_tmp/ +-test_tmp/ +- +-# Coverage files +-.coverage +-htmlcov/ +-ete +diff -ruN /tmp/ete/.travis.yml /tmp/ete_new/.travis.yml +--- /tmp/ete/.travis.yml 2020-10-14 12:57:02.475810686 +0200 ++++ /tmp/ete_new/.travis.yml 1970-01-01 01:00:00.000000000 +0100 +@@ -1,43 +0,0 @@ +-language: python +-sudo: false +- +-services: +- - xvfb +- +-python: +- #- "2.7" +- #- "3.4" +- - "3.5" +- - "3.6" +- +-cache: +- directories: +- - test_tmp +- +-install: +- - ./run_tests.sh -s --setup-only -v "$TRAVIS_PYTHON_VERSION" +- +-before_script: +- # Ensure tags are available on the cloned repository +- - git fetch --tags --depth=50 +- +- # Start xvfb +- # - "export DISPLAY=:99.0" +- # - "sh -e /etc/init.d/xvfb start" +- # - sleep 3 +- +-script: +- - ./run_tests.sh --test-only -sv "$TRAVIS_PYTHON_VERSION" +- # - if [[ $TRAVIS_PYTHON_VERSION == 2.7 ]]; then ./run_tests.sh --qt4 -sv "$TRAVIS_PYTHON_VERSION" ; fi +- - if [[ $TRAVIS_PYTHON_VERSION == 2.7 ]]; then ./run_tests.sh -sv "$TRAVIS_PYTHON_VERSION" ; fi +- #- coverage run -m ete3.test.test_api +- #- coverage run -a -m ete3.test.test_ete_evol # too heavy for travis +- #- coverage run -a -m ete3.test.test_ete_build # too heavy for travis +- +-after_success: +- - coveralls +-# branches: +-# only: +-# - master +-# - "3.0" +-# - "2.3" diff --git a/recipe/meta.yaml b/recipe/meta.yaml index f3bbcf5..7737454 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -11,6 +11,8 @@ source: fn: {{ name }}-{{ version }}.{{ bundle }} url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.{{ bundle }} sha256: {{ hash }} + patches: + - import.patch build: noarch: python From da7f7c5bae249ea2300061d9528f4f5f55ef7828 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Wed, 14 Oct 2020 13:54:26 +0200 Subject: [PATCH 5/7] pyqt <5 --- recipe/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipe/meta.yaml b/recipe/meta.yaml index 7737454..82a15b4 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -30,7 +30,7 @@ requirements: - six - lxml - numpy - - pyqt >=4.11.* + - pyqt >=4.11.*,<5 - scipy - xorg-libxext - xorg-xextproto From 11e5ca6119954899d43f39b9bac42368a6c81652 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Wed, 14 Oct 2020 14:10:32 +0200 Subject: [PATCH 6/7] more patching --- recipe/import.patch | 43 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/recipe/import.patch b/recipe/import.patch index fe94e43..d568393 100644 --- a/recipe/import.patch +++ b/recipe/import.patch @@ -48,6 +48,49 @@ diff -ruN /tmp/ete/ete3/__init__.py /tmp/ete_new/ete3/__init__.py try: from .version import __version__ +Binary files /tmp/ete/ete3/.__init__.py.swp and /tmp/ete_new/ete3/.__init__.py.swp differ +diff -ruN /tmp/ete/ete3/tools/ete_view.py /tmp/ete_new/ete3/tools/ete_view.py +--- /tmp/ete/ete3/tools/ete_view.py 2020-10-14 12:57:02.539810759 +0200 ++++ /tmp/ete_new/ete3/tools/ete_view.py 2020-10-14 14:09:20.615514307 +0200 +@@ -45,7 +45,7 @@ + from collections import defaultdict + + from .common import log, POSNAMES, node_matcher, src_tree_iterator +-from .. import (Tree, PhyloTree, TextFace, RectFace, faces, TreeStyle, CircleFace, AttrFace, ++from .. import (Tree, PhyloTree, SeqMotifFace, TextFace, RectFace, TreeStyle, CircleFace, AttrFace, + add_face_to_node, random_color) + from six.moves import map + +@@ -417,15 +417,15 @@ + fstyle = f.get('fstyle', None)) + + elif f["ftype"] == "fullseq": +- F = faces.SeqMotifFace(seq=fvalue, seq_format="seq", ++ F = SeqMotifFace(seq=fvalue, seq_format="seq", + gap_format="line", + height=fsize) + elif f["ftype"] == "compactseq": +- F = faces.SeqMotifFace(seq=fvalue, seq_format="compactseq", ++ F = SeqMotifFace(seq=fvalue, seq_format="compactseq", + gap_format="compactseq", + height=fsize) + elif f["ftype"] == "blockseq": +- F = faces.SeqMotifFace(seq=fvalue, ++ F = SeqMotifFace(seq=fvalue, + height=fsize, + fgcolor=fcolor or "slategrey", + bgcolor=fbgcolor or "slategrey", +@@ -438,7 +438,7 @@ + rad = fsize + else: + rad = fsize * v +- F = faces.CircleFace(radius=rad, style="sphere", ++ F = CircleFace(radius=rad, style="sphere", + color=fcolor or "steelblue") + + elif f["ftype"] == "heatmap": +Binary files /tmp/ete/ete3/tools/.ete_view.py.swp and /tmp/ete_new/ete3/tools/.ete_view.py.swp differ +Binary files /tmp/ete/ete3/treeview/.faces.py.swp and /tmp/ete_new/ete3/treeview/.faces.py.swp differ diff -ruN /tmp/ete/.git/config /tmp/ete_new/.git/config --- /tmp/ete/.git/config 2020-10-14 12:57:02.423810626 +0200 +++ /tmp/ete_new/.git/config 1970-01-01 01:00:00.000000000 +0100 From 490106d14b257b0e03f51aeb3043077512109ee6 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Wed, 14 Oct 2020 14:16:37 +0200 Subject: [PATCH 7/7] Revert "pyqt <5" This reverts commit da7f7c5bae249ea2300061d9528f4f5f55ef7828. --- recipe/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipe/meta.yaml b/recipe/meta.yaml index 82a15b4..7737454 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -30,7 +30,7 @@ requirements: - six - lxml - numpy - - pyqt >=4.11.*,<5 + - pyqt >=4.11.* - scipy - xorg-libxext - xorg-xextproto