From e335ca9ff1a0589e6545c9edd666be09726859ae Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hadrien=20Gourl=C3=A9?= Date: Thu, 15 Feb 2024 16:32:12 +0100 Subject: [PATCH 1/9] version bump (2.0.0) --- iss/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/iss/version.py b/iss/version.py index e4adfb8..8c0d5d5 100644 --- a/iss/version.py +++ b/iss/version.py @@ -1 +1 @@ -__version__ = "1.6.0" +__version__ = "2.0.0" From d0e18884a3de07d96ff84ca97d38aacbd2e9e998 Mon Sep 17 00:00:00 2001 From: stefanlelieveld Date: Mon, 19 Feb 2024 10:55:19 +0100 Subject: [PATCH 2/9] Updated dockerfile --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index d091a08..133e63b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,10 +1,10 @@ FROM python:3 -LABEL maintainer "Hadrien Gourlé " +MAINTAINER "Hadrien Gourlé " WORKDIR /usr/src/app COPY . . RUN pip install --no-cache-dir . -CMD [ "iss" ] +ENTRYPOINT [ "iss" ] From de245f17dbbcf075c2b5ac926fdb49c4826bf92a Mon Sep 17 00:00:00 2001 From: stefanlelieveld Date: Mon, 19 Feb 2024 15:33:14 +0100 Subject: [PATCH 3/9] Added script to build multi-architecture (AMD + ARM) docker image and push to registry --- docker-build.sh | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 docker-build.sh diff --git a/docker-build.sh b/docker-build.sh new file mode 100644 index 0000000..a53d625 --- /dev/null +++ b/docker-build.sh @@ -0,0 +1,26 @@ +#!/bin/bash + +# set image registry and image name +REGISTRY="" +IMAGE_NAME="insilicoseq" + +# Version-build: sync version form setup.py +VERSION=$(python3 setup.py --version) + +# create custom builder for multi-arch image. Default docker-builder can not create multi-arch builds. +docker buildx \ +create \ +--name inSilicoSeq-builder \ +--use + +# build + push multi-arch image for AMD and ARM architectures +docker build . \ +--builder inSilicoSeq-builder \ +--platform linux/amd64,linux/arm64 \ +-t "${REGISTRY}/${IMAGE_NAME}:${VERSION}" \ +--provenance=false \ +--push + +# remove custom inSilicoSeq-builder +docker buildx \ +rm inSilicoSeq-builder \ No newline at end of file From cbc4c6c1ffe5890963012088d225071052ef5e0e Mon Sep 17 00:00:00 2001 From: stefanlelieveld Date: Tue, 20 Feb 2024 16:06:42 +0100 Subject: [PATCH 4/9] Removed Dockerfile and docker-build.sh. We will start using the Bioconda biocontainer instead --- Dockerfile | 10 ---------- docker-build.sh | 26 -------------------------- 2 files changed, 36 deletions(-) delete mode 100644 Dockerfile delete mode 100644 docker-build.sh diff --git a/Dockerfile b/Dockerfile deleted file mode 100644 index 133e63b..0000000 --- a/Dockerfile +++ /dev/null @@ -1,10 +0,0 @@ -FROM python:3 - -MAINTAINER "Hadrien Gourlé " - -WORKDIR /usr/src/app - -COPY . . -RUN pip install --no-cache-dir . - -ENTRYPOINT [ "iss" ] diff --git a/docker-build.sh b/docker-build.sh deleted file mode 100644 index a53d625..0000000 --- a/docker-build.sh +++ /dev/null @@ -1,26 +0,0 @@ -#!/bin/bash - -# set image registry and image name -REGISTRY="" -IMAGE_NAME="insilicoseq" - -# Version-build: sync version form setup.py -VERSION=$(python3 setup.py --version) - -# create custom builder for multi-arch image. Default docker-builder can not create multi-arch builds. -docker buildx \ -create \ ---name inSilicoSeq-builder \ ---use - -# build + push multi-arch image for AMD and ARM architectures -docker build . \ ---builder inSilicoSeq-builder \ ---platform linux/amd64,linux/arm64 \ --t "${REGISTRY}/${IMAGE_NAME}:${VERSION}" \ ---provenance=false \ ---push - -# remove custom inSilicoSeq-builder -docker buildx \ -rm inSilicoSeq-builder \ No newline at end of file From 5e5b939abb00a9c3360c7309ef929a71c388f13e Mon Sep 17 00:00:00 2001 From: stefanlelieveld Date: Tue, 20 Feb 2024 16:10:47 +0100 Subject: [PATCH 5/9] Updated README.md to include the link to the biocontainers repo --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 369a637..1a63e0c 100644 --- a/README.md +++ b/README.md @@ -37,7 +37,7 @@ _Note:_ Insilicoseq requires python >= 3.5 Alternatively, with docker: ```shell -docker pull hadrieng/insilicoseq:latest +docker pull quay.io/biocontainers/insilicoseq:2.0.0--pyh7cba7a3_0 ``` For more installation options, please refer to the full [documentation](http://insilicoseq.readthedocs.io) From 49bc79309b568d0c1378487ebeeed5346f0fb83a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hadrien=20Gourl=C3=A9?= Date: Thu, 22 Feb 2024 11:20:52 +0100 Subject: [PATCH 6/9] updated docker instructions on readthedocs --- doc/iss/install.rst | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/iss/install.rst b/doc/iss/install.rst index a80dd58..27604a7 100644 --- a/doc/iss/install.rst +++ b/doc/iss/install.rst @@ -63,15 +63,16 @@ If you wish to use InSilicoSeq using docker .. code-block:: bash - docker pull hadrieng/insilicoseq:latest + docker pull docker pull quay.io/biocontainers/insilicoseq: +Where should be chosen amongst the tags available on `quay.io `_ . To use InSilicoSeq with docker, you need to provide a `volume` to the ``docker run`` command. Given with the ``-v`` option, the volume is your way of exchanging data (in this case, your input and output files) with the docker container. .. code-block:: bash docker run -v /Users/hadrien/data:/mnt/data -it --rm \ - hadrieng/insilicoseq iss generate \ + quay.io/biocontainers/insilicoseq: iss generate \ --genomes /mnt/data/genomes.fasta -m miseq \ -o /mnt/data/reads From 7858571967a72385157b1a56c619fe737727204c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hadrien=20Gourl=C3=A9?= Date: Fri, 23 Feb 2024 09:38:22 +0100 Subject: [PATCH 7/9] fix crash when using --coverage (#253) --- iss/app.py | 2 +- iss/generator.py | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/iss/app.py b/iss/app.py index 12656a0..bbcdbdd 100644 --- a/iss/app.py +++ b/iss/app.py @@ -64,7 +64,7 @@ def generate_reads(args): if readcount_dic is not None: n_reads = sum(readcount_dic.values()) logger.info("Generating %s reads" % n_reads) - elif not (args.coverage or args.coverage_file): + else: n_reads = util.convert_n_reads(args.n_reads) logger.info("Generating %s reads" % n_reads) diff --git a/iss/generator.py b/iss/generator.py index f948d7b..70033f5 100644 --- a/iss/generator.py +++ b/iss/generator.py @@ -560,7 +560,6 @@ def load_readcount_or_abundance( abundance_dic = abundance.parse_abundance_file(coverage_file) elif coverage in abundance_dispatch: # todo coverage distribution with --draft - logger.warning("--coverage is an experimental feature") logger.info("Using %s coverage distribution" % coverage) if draft: abundance_dic = abundance.draft( From e2bc0d89691ee63f9cf33ee097b44a2fe37fbd5f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hadrien=20Gourl=C3=A9?= Date: Fri, 23 Feb 2024 09:41:54 +0100 Subject: [PATCH 8/9] version bump (2.0.1) --- iss/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/iss/version.py b/iss/version.py index 8c0d5d5..159d48b 100644 --- a/iss/version.py +++ b/iss/version.py @@ -1 +1 @@ -__version__ = "2.0.0" +__version__ = "2.0.1" From b929c9b6f91c6899c40c22074b7e314be8b1ec15 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 21 May 2024 06:06:04 +0000 Subject: [PATCH 9/9] --- updated-dependencies: - dependency-name: requests dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- Pipfile.lock | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index 07e8e12..f7b9b1f 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -51,11 +51,11 @@ }, "certifi": { "hashes": [ - "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1", - "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474" + "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f", + "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1" ], "markers": "python_version >= '3.6'", - "version": "==2023.11.17" + "version": "==2024.2.2" }, "charset-normalizer": { "hashes": [ @@ -155,11 +155,11 @@ }, "idna": { "hashes": [ - "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4", - "sha256:90b77e79eaa3eba6de819a0c442c0b4ceefc341a7a2ab77d7562bf49f425c5c2" + "sha256:028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc", + "sha256:82fee1fc78add43492d3a1898bfa6d8a904cc97d8427f683ed8e798d07761aa0" ], "markers": "python_version >= '3.5'", - "version": "==3.4" + "version": "==3.7" }, "numpy": { "hashes": [ @@ -240,12 +240,12 @@ }, "requests": { "hashes": [ - "sha256:58cd2187c01e70e6e26505bca751777aa9f2ee0b7f4300988b709f44e013003f", - "sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1" + "sha256:f2c3881dddb70d056c5bd7600a4fae312b2a300e39be6a118d30b90bd27262b5", + "sha256:fa5490319474c82ef1d2c9bc459d3652e3ae4ef4c4ebdd18a21145a47ca4b6b8" ], "index": "pypi", - "markers": "python_version >= '3.7'", - "version": "==2.31.0" + "markers": "python_version >= '3.8'", + "version": "==2.32.0" }, "scipy": { "hashes": [ @@ -281,12 +281,12 @@ }, "urllib3": { "hashes": [ - "sha256:55901e917a5896a349ff771be919f8bd99aff50b79fe58fec595eb37bbc56bb3", - "sha256:df7aa8afb0148fa78488e7899b2c59b5f4ffcfa82e6c54ccb9dd37c1d7b52d54" + "sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d", + "sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19" ], "index": "pypi", "markers": "python_version >= '3.8'", - "version": "==2.1.0" + "version": "==2.2.1" } }, "develop": {