From 91e88b46b02efc90c7bbf38b9a10c5ea0154d5cd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sun, 21 May 2023 19:57:16 +0200 Subject: [PATCH 01/17] use bioconda-utils 2.1.0 --- common.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/common.sh b/common.sh index e64ef35..ed8ae6f 100644 --- a/common.sh +++ b/common.sh @@ -1,4 +1,4 @@ MINICONDA_VER=py37_4.8.3 -BIOCONDA_UTILS_TAG=v2.0.0 +BIOCONDA_UTILS_TAG=v2.1.0 MAMBAFORGE_VER=23.1.0-1 -MAMBAFORGE_INSTALLATION_DIR="/opt/mambaforge" \ No newline at end of file +MAMBAFORGE_INSTALLATION_DIR="/opt/mambaforge" From af1b2c806891b1bcf8432568b67ab496af2d88e7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Mon, 22 May 2023 10:55:15 +0200 Subject: [PATCH 02/17] use bioconda-utils 2.2.0 --- common.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common.sh b/common.sh index ed8ae6f..11afb17 100644 --- a/common.sh +++ b/common.sh @@ -1,4 +1,4 @@ MINICONDA_VER=py37_4.8.3 -BIOCONDA_UTILS_TAG=v2.1.0 +BIOCONDA_UTILS_TAG=v2.2.0 MAMBAFORGE_VER=23.1.0-1 MAMBAFORGE_INSTALLATION_DIR="/opt/mambaforge" From 5ec0199cdd53ee53b275d4750e73d728c4625e24 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Mon, 22 May 2023 21:41:26 +0200 Subject: [PATCH 03/17] use v2.2.1 --- common.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common.sh b/common.sh index 11afb17..4985bd5 100644 --- a/common.sh +++ b/common.sh @@ -1,4 +1,4 @@ MINICONDA_VER=py37_4.8.3 -BIOCONDA_UTILS_TAG=v2.2.0 +BIOCONDA_UTILS_TAG=v2.2.1 MAMBAFORGE_VER=23.1.0-1 MAMBAFORGE_INSTALLATION_DIR="/opt/mambaforge" From a23bbcd13a39a9a71c7c6ad60ab988cb98bb4355 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Tue, 23 May 2023 17:55:46 +0200 Subject: [PATCH 04/17] dbg: use fix branch --- common.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common.sh b/common.sh index 4985bd5..2440c4e 100644 --- a/common.sh +++ b/common.sh @@ -1,4 +1,4 @@ MINICONDA_VER=py37_4.8.3 -BIOCONDA_UTILS_TAG=v2.2.1 +BIOCONDA_UTILS_TAG=fix/build-failure-logs MAMBAFORGE_VER=23.1.0-1 MAMBAFORGE_INSTALLATION_DIR="/opt/mambaforge" From 6cbc40e5afa5bffec614913bf84bf1084426b439 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Tue, 4 Jul 2023 10:41:59 +0200 Subject: [PATCH 05/17] sync bulk with master --- common.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common.sh b/common.sh index 8227fd8..29cfc4d 100644 --- a/common.sh +++ b/common.sh @@ -1,4 +1,4 @@ MINICONDA_VER=py37_4.8.3 -BIOCONDA_UTILS_TAG=v2.3.1 +BIOCONDA_UTILS_TAG=v2.3.2 MAMBAFORGE_VER=23.1.0-1 MAMBAFORGE_INSTALLATION_DIR="/opt/mambaforge" From 464cf9d7c4b7cd01905676971392682e35e14200 Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Fri, 7 Jul 2023 08:41:32 +0200 Subject: [PATCH 06/17] Update common.sh --- common.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common.sh b/common.sh index 29cfc4d..7db8a0b 100644 --- a/common.sh +++ b/common.sh @@ -1,4 +1,4 @@ MINICONDA_VER=py37_4.8.3 -BIOCONDA_UTILS_TAG=v2.3.2 +BIOCONDA_UTILS_TAG=v2.3.3 MAMBAFORGE_VER=23.1.0-1 MAMBAFORGE_INSTALLATION_DIR="/opt/mambaforge" From 2845d451224cbb81967473aa178926039c6e0b69 Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Sat, 15 Jul 2023 21:52:57 +0200 Subject: [PATCH 07/17] Update common.sh --- common.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common.sh b/common.sh index 7db8a0b..1fda7b5 100644 --- a/common.sh +++ b/common.sh @@ -1,4 +1,4 @@ MINICONDA_VER=py37_4.8.3 -BIOCONDA_UTILS_TAG=v2.3.3 +BIOCONDA_UTILS_TAG=v2.3.4 MAMBAFORGE_VER=23.1.0-1 MAMBAFORGE_INSTALLATION_DIR="/opt/mambaforge" From 5dd3689674fe121365b3510b10d339bc1c81d908 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 24 Aug 2023 20:34:17 +0200 Subject: [PATCH 08/17] Update common.sh --- common.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common.sh b/common.sh index 1fda7b5..bb189a7 100644 --- a/common.sh +++ b/common.sh @@ -1,4 +1,4 @@ MINICONDA_VER=py37_4.8.3 -BIOCONDA_UTILS_TAG=v2.3.4 +BIOCONDA_UTILS_TAG=v2.4.0 MAMBAFORGE_VER=23.1.0-1 MAMBAFORGE_INSTALLATION_DIR="/opt/mambaforge" From 94cb7347b15912e5d3cb5421880f4e01bb76d5a3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 4 Oct 2023 14:31:43 +0200 Subject: [PATCH 09/17] Use bioconda-utils 2.5.0 for bulk (#39) --- common.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common.sh b/common.sh index bb189a7..c0ea7f1 100644 --- a/common.sh +++ b/common.sh @@ -1,4 +1,4 @@ MINICONDA_VER=py37_4.8.3 -BIOCONDA_UTILS_TAG=v2.4.0 +BIOCONDA_UTILS_TAG=v2.5.0 MAMBAFORGE_VER=23.1.0-1 MAMBAFORGE_INSTALLATION_DIR="/opt/mambaforge" From 132bb481cc6e42dc9a8686aca3a5e64a15f855d5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Mon, 9 Oct 2023 09:26:41 +0200 Subject: [PATCH 10/17] Update to bioconda-utils 2.6.0 --- common.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common.sh b/common.sh index c0ea7f1..7a93485 100644 --- a/common.sh +++ b/common.sh @@ -1,4 +1,4 @@ MINICONDA_VER=py37_4.8.3 -BIOCONDA_UTILS_TAG=v2.5.0 +BIOCONDA_UTILS_TAG=v2.6.0 MAMBAFORGE_VER=23.1.0-1 MAMBAFORGE_INSTALLATION_DIR="/opt/mambaforge" From 601e85402a339ce824c1cf239d306aaafef74869 Mon Sep 17 00:00:00 2001 From: "Alicia A. Evans" <108547992+aliciaaevans@users.noreply.github.com> Date: Thu, 9 Nov 2023 14:23:53 -0500 Subject: [PATCH 11/17] Update bulk to bioconda-utils version 2.9.0 (#44) Need this for ARM bulk CI to check for `linux-aarch64` in `extra.additional-platforms`. --- common.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common.sh b/common.sh index 7a93485..47c3191 100644 --- a/common.sh +++ b/common.sh @@ -1,4 +1,4 @@ MINICONDA_VER=py37_4.8.3 -BIOCONDA_UTILS_TAG=v2.6.0 +BIOCONDA_UTILS_TAG=v2.9.0 MAMBAFORGE_VER=23.1.0-1 MAMBAFORGE_INSTALLATION_DIR="/opt/mambaforge" From f0614fd51b364917d40e3a5693b8d0d75cec12d4 Mon Sep 17 00:00:00 2001 From: "Alicia A. Evans" <108547992+aliciaaevans@users.noreply.github.com> Date: Thu, 14 Dec 2023 08:48:23 -0500 Subject: [PATCH 12/17] Update Bulk to bioconda-utils 2.11.1 (#47) --- common.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common.sh b/common.sh index 3da41b2..c3e2a79 100644 --- a/common.sh +++ b/common.sh @@ -1,3 +1,3 @@ -BIOCONDA_UTILS_TAG=v2.11.0 +BIOCONDA_UTILS_TAG=v2.11.1 MAMBAFORGE_VER=23.1.0-1 MAMBAFORGE_INSTALLATION_DIR="/opt/mambaforge" From 12af16319486336580fb7e55b2d8a3f2aa862974 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 27 Mar 2024 10:34:01 +0100 Subject: [PATCH 13/17] fix: update to bioconda-utils 2.13.1 --- common.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common.sh b/common.sh index 2a746c7..b758b1f 100644 --- a/common.sh +++ b/common.sh @@ -1,3 +1,3 @@ -BIOCONDA_UTILS_TAG=v2.13.0 +BIOCONDA_UTILS_TAG=v2.13.1 MAMBAFORGE_VER=23.1.0-1 MAMBAFORGE_INSTALLATION_DIR="/opt/mambaforge" From 505141f7ccf94683777bdcb597219a18ca3b35e9 Mon Sep 17 00:00:00 2001 From: Marcel Bargull Date: Wed, 27 Mar 2024 11:43:41 +0100 Subject: [PATCH 14/17] update to bioconda-utils v2.13.2 (#50) > ### Bug Fixes > > * update anaconda-client=1.12 to fix uploads ([#970](https://www.github.com/bioconda/bioconda-utils/issues/970)) ([06dcacc](https://www.github.com/bioconda/bioconda-utils/commit/06dcacca60c17c1a97770e14ae6348ac7acbe9a6)) refs: - https://github.com/bioconda/bioconda-utils/releases/tag/v2.13.2 - https://github.com/bioconda/bioconda-utils/pull/970 Signed-off-by: Marcel Bargull --- common.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common.sh b/common.sh index b758b1f..149d502 100644 --- a/common.sh +++ b/common.sh @@ -1,3 +1,3 @@ -BIOCONDA_UTILS_TAG=v2.13.1 +BIOCONDA_UTILS_TAG=v2.13.2 MAMBAFORGE_VER=23.1.0-1 MAMBAFORGE_INSTALLATION_DIR="/opt/mambaforge" From 35412e70ca0ebfa13f1b6e2c75e399a29f1bf7d9 Mon Sep 17 00:00:00 2001 From: "Alicia A. Evans" <108547992+aliciaaevans@users.noreply.github.com> Date: Mon, 3 Jun 2024 17:53:55 -0400 Subject: [PATCH 15/17] Bulk: bioconda-utils v3.3.0 (#55) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Update bulk to match master - Use new bioconda-utils version with updated pinnings --------- Signed-off-by: Marcel Bargull Co-authored-by: Johannes Köster Co-authored-by: Marcel Bargull Co-authored-by: Marcel Bargull --- common.sh | 4 ++-- configure-conda.sh | 6 ++++-- install-and-set-up-conda.sh | 13 +++++-------- 3 files changed, 11 insertions(+), 12 deletions(-) diff --git a/common.sh b/common.sh index 149d502..89997ae 100644 --- a/common.sh +++ b/common.sh @@ -1,3 +1,3 @@ -BIOCONDA_UTILS_TAG=v2.13.2 -MAMBAFORGE_VER=23.1.0-1 +BIOCONDA_UTILS_TAG=v3.3.0 +MAMBAFORGE_VER=24.3.0-0 MAMBAFORGE_INSTALLATION_DIR="/opt/mambaforge" diff --git a/configure-conda.sh b/configure-conda.sh index b8393c4..5d2bcda 100644 --- a/configure-conda.sh +++ b/configure-conda.sh @@ -21,11 +21,13 @@ then fi conda config --set always_yes yes -conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge +conda config --remove channels defaults || true conda config --set channel_priority strict +# .conda support is pending https://github.com/conda/infrastructure/issues/950 +# conda config --set conda_build.pkg_format 2 if [ ${BIOCONDA_DISABLE_BUILD_PREP:=0} == 0 ]; then conda config --add channels "file://${MAMBAFORGE_INSTALLATION_DIR}/conda-bld" -fi \ No newline at end of file +fi diff --git a/install-and-set-up-conda.sh b/install-and-set-up-conda.sh index 3defe66..8e29135 100644 --- a/install-and-set-up-conda.sh +++ b/install-and-set-up-conda.sh @@ -5,7 +5,6 @@ set -e # - Installs mambaforge to ${HOME}/mambaforge. Version is determined by common.sh, # which is downloaded at runtime. # - Sets channel order and sets strict channel priority -# - Installs mamba into the base env # - Installs bioconda-utils into a "bioconda" env (unless # $BIOCONDA_DISABLE_BUILD_PREP=1). Version is determined by common.sh. # - Sets up local channel to have highest priority (unless $BIOCONDA_DISABLE_BUILD_PREP=1) @@ -44,8 +43,6 @@ if [[ $(uname) == "Darwin" ]]; then sudo chown -R $USER $(dirname $MAMBAFORGE_INSTALLATION_DIR) # conda-forge-ci-setup does some additional setup for Mac. - # Installing bioconda-utils and conda-forge-ci-setup with conda causes dependency conflicts. - # Installing bioconda-utils and conda-forge-ci-setup with mamba works fine. BIOCONDA_ADDITIONAL_INSTALL_PKGS="conda-forge-ci-setup" else mkdir -p $(dirname $MAMBAFORGE_INSTALLATION_DIR) @@ -67,8 +64,6 @@ export PATH="${MAMBAFORGE_INSTALLATION_DIR}/bin:${PATH}" # disable build preparation here because we don't yet have the local channel from conda-build BIOCONDA_DISABLE_BUILD_PREP=1 bash configure-conda.sh -mamba install mamba -y - # By default, for building packages, we install bioconda-utils. However when # testing bioconda-utils itself, we don't want to install a release, in # which case set BIOCONDA_DISABLE_BUILD_PREP to a non-zero value. @@ -78,9 +73,9 @@ if [ ${BIOCONDA_DISABLE_BUILD_PREP:=0} == 0 ]; then source ${MAMBAFORGE_INSTALLATION_DIR}/etc/profile.d/mamba.sh # set up env with all dependencies - mamba create -n bioconda -y --file https://raw.githubusercontent.com/bioconda/bioconda-utils/$BIOCONDA_UTILS_TAG/bioconda_utils/bioconda_utils-requirements.txt $BIOCONDA_ADDITIONAL_INSTALL_PKGS + conda create -n bioconda -y --file https://raw.githubusercontent.com/bioconda/bioconda-utils/$BIOCONDA_UTILS_TAG/bioconda_utils/bioconda_utils-requirements.txt $BIOCONDA_ADDITIONAL_INSTALL_PKGS - mamba activate bioconda + conda activate bioconda # install bioconda-utils itself via pip (this way we don't always have to wait for the conda package to be built before being able to fix things here) pip install git+https://github.com/bioconda/bioconda-utils.git@$BIOCONDA_UTILS_TAG @@ -88,7 +83,9 @@ if [ ${BIOCONDA_DISABLE_BUILD_PREP:=0} == 0 ]; then # Set local channel as highest priority (requires conda-build, which is # installed as a dependency of bioconda-utils) mkdir -p "${MAMBAFORGE_INSTALLATION_DIR}/conda-bld/{noarch,linux-64,osx-64,linux-aarch64,osx-arm64}" - conda index "${MAMBAFORGE_INSTALLATION_DIR}/conda-bld" + # The base installation does not include conda-index, so use "command conda" to run bioconda + # env's "conda index". + command conda index "${MAMBAFORGE_INSTALLATION_DIR}/conda-bld" conda config --add channels "file://${MAMBAFORGE_INSTALLATION_DIR}/conda-bld" fi From 7210a1944abff95bbbae83620053b45ee765ec19 Mon Sep 17 00:00:00 2001 From: aliciaaevans Date: Thu, 6 Jun 2024 16:15:43 -0400 Subject: [PATCH 16/17] bump to bioconda-utils 3.3.1 --- common.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common.sh b/common.sh index 89997ae..0f960ed 100644 --- a/common.sh +++ b/common.sh @@ -1,3 +1,3 @@ -BIOCONDA_UTILS_TAG=v3.3.0 +BIOCONDA_UTILS_TAG=v3.3.1 MAMBAFORGE_VER=24.3.0-0 MAMBAFORGE_INSTALLATION_DIR="/opt/mambaforge" From b68da1a29e06e3867ab0e3a64c66e82c3e2a9320 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Sat, 8 Jun 2024 21:38:30 +0000 Subject: [PATCH 17/17] export macOS env vars While these are specified in bioconda_utils' bioconda_utils-conda_build_config.yaml, they do not make it out into environment variables. Yet they are required for `run_conda_forge_build_setup` to set the correct deployment target, so we set them here. --- common.sh | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/common.sh b/common.sh index 0f960ed..9b0b450 100644 --- a/common.sh +++ b/common.sh @@ -1,3 +1,14 @@ BIOCONDA_UTILS_TAG=v3.3.1 MAMBAFORGE_VER=24.3.0-0 MAMBAFORGE_INSTALLATION_DIR="/opt/mambaforge" +platform=$(uname -s) +arch=$(uname -m) +if [[ "$platform" == "Darwin" ]]; then + if [[ "$arch" == "arm64" ]]; then + export MACOSX_DEPLOYMENT_TARGET=11 + export MACOSX_SDK_VERSION=11 + elif [[ "$arch" == 'x86_64' ]]; then + export MACOSX_DEPLOYMENT_TARGET=10.13 + export MACOSX_SDK_VERSION=10.13 + fi +fi