[med-svn] [Git][med-team/augur][upstream] New upstream version 23.1.1
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Thu Nov 23 14:15:12 GMT 2023
Étienne Mollier pushed to branch upstream at Debian Med / augur
Commits:
f645e910 by Étienne Mollier at 2023-11-23T15:07:17+01:00
New upstream version 23.1.1
- - - - -
9 changed files:
- .github/workflows/ci.yaml
- .github/workflows/release.yaml
- .github/workflows/sync-redirects.yaml
- CHANGES.md
- augur/__version__.py
- augur/io/metadata.py
- docs/contribute/DEV_DOCS.md
- docs/index.rst
- setup.py
Changes:
=====================================
.github/workflows/ci.yaml
=====================================
@@ -45,7 +45,7 @@ jobs:
COVERAGE_FILE: ${{ github.workspace }}/.coverage at python=${{ matrix.python-version }},biopython=${{ matrix.biopython-version || 'latest' }}
COVERAGE_RCFILE: ${{ github.workspace }}/.coveragerc
steps:
- - uses: actions/checkout at v3
+ - uses: actions/checkout at v4
- uses: conda-incubator/setup-miniconda at v2
with:
python-version: ${{ matrix.python-version }}
@@ -85,7 +85,9 @@ jobs:
- { pathogen: avian-flu, build-args: auspice/flu_avian_h5n1_ha.json }
- { pathogen: ebola }
- { pathogen: lassa }
- - { pathogen: monkeypox }
+ # Disable mpox CI until pathogen-repo-ci supports custom build directories
+ # See issue https://github.com/nextstrain/.github/issues/63
+ # - { pathogen: mpox }
- { pathogen: mumps }
- {
pathogen: ncov,
@@ -103,7 +105,7 @@ jobs:
run:
shell: bash -l {0}
steps:
- - uses: actions/checkout at v3
+ - uses: actions/checkout at v4
with:
path: ./augur
@@ -121,7 +123,7 @@ jobs:
- run: pip install ./augur
- - uses: actions/checkout at v3
+ - uses: actions/checkout at v4
with:
repository: nextstrain/${{ matrix.pathogen }}
path: ./pathogen-repo
@@ -154,7 +156,7 @@ jobs:
needs: [pytest-cram]
runs-on: ubuntu-latest
steps:
- - uses: actions/checkout at v3
+ - uses: actions/checkout at v4
- uses: actions/setup-python at v4
- run: pip install coverage
=====================================
.github/workflows/release.yaml
=====================================
@@ -10,7 +10,7 @@ jobs:
run:
runs-on: ubuntu-latest
steps:
- - uses: actions/checkout at v3
+ - uses: actions/checkout at v4
with:
# Fetch all branches and tags.
fetch-depth: 0
=====================================
.github/workflows/sync-redirects.yaml
=====================================
@@ -15,7 +15,7 @@ jobs:
sync:
runs-on: ubuntu-latest
steps:
- - uses: actions/checkout at v3
+ - uses: actions/checkout at v4
- uses: actions/setup-python at v4
- name: Upgrade Python toolchain
=====================================
CHANGES.md
=====================================
@@ -3,6 +3,16 @@
## __NEXT__
+## 23.1.1 (7 November 2023)
+
+### Bug Fixes
+
+* Fix Python 3.11 installation for Conda environments. [#1334][] (@victorlin)
+* Bump `pyfastx` dependency to major versions 1 and 2. [#1335][] (@victorlin)
+
+[#1334]: https://github.com/nextstrain/augur/issues/1334
+[#1335]: https://github.com/nextstrain/augur/pull/1335
+
## 23.1.0 (22 September 2023)
### Features
=====================================
augur/__version__.py
=====================================
@@ -1,4 +1,4 @@
-__version__ = '23.1.0'
+__version__ = '23.1.1'
def is_augur_version_compatible(version):
=====================================
augur/io/metadata.py
=====================================
@@ -336,10 +336,11 @@ def read_metadata_with_sequences(metadata, metadata_delimiters, fasta, seq_id_co
else:
processed_metadata_ids.add(seq_id)
- # Skip records that do not have a matching sequence
- # TODO: change this to try/except to fetch sequences and catch
- # KeyError for non-existing sequences when https://github.com/lmdu/pyfastx/issues/50 is resolved
- if seq_id not in sequence_ids:
+ try:
+ sequence_record = sequences[seq_id]
+ except KeyError:
+ # Skip records that do not have a matching sequence
+
# Immediately raise an error if requested to error on the first unmatched record
if unmatched_reporting is DataErrorMethod.ERROR_FIRST:
raise AugurError(f"Encountered metadata record {seq_id!r} without a matching sequence.")
=====================================
docs/contribute/DEV_DOCS.md
=====================================
@@ -212,7 +212,7 @@ If there are changes to the Python version or dependency list:
##### 5. Build/Release Nextstrain/conda-base
1. Wait for the bioconda-recipe PR to be merged.
-2. Wait for the new version of Augur to be available in on bioconda.
+2. Wait for the new version of Augur to be available [on bioconda](https://anaconda.org/bioconda/augur).
3. Manually run the [conda-base CI workflow](https://github.com/nextstrain/conda-base/actions/workflows/ci.yaml) on the `main` branch.
4. Ensure workflow runs successfully.
=====================================
docs/index.rst
=====================================
@@ -19,9 +19,6 @@ It provides a collection of commands which are designed to be composable into la
Augur originated as part of `Nextstrain <https://nextstrain.org>`__, an open-source project to harness the scientific and public health potential of pathogen genome data.
All source code is available on `GitHub <https://github.com/nextstrain/augur>`__.
-.. note:: We have just released version 6 of augur -- `check our upgrading guide <releases/migrating-v5-v6.html>`__
-
-
Augur is composed of a series of modules and different workflows will use different parts of the pipeline.
A selection of augur modules and different possible entry points are illustrated below.
=====================================
setup.py
=====================================
@@ -62,7 +62,7 @@ setuptools.setup(
"packaging >=19.2",
"pandas >=1.0.0, ==1.*",
"phylo-treetime >=0.10.0, <0.12",
- "pyfastx >=0.8.4, ==0.8.*",
+ "pyfastx >=1.0.0, <3.0",
"scipy ==1.*",
"xopen[zstd] >=1.7.0, ==1.*"
],
View it on GitLab: https://salsa.debian.org/med-team/augur/-/commit/f645e910276b5b6ed9116a19e4a22dec1c10f24f
--
View it on GitLab: https://salsa.debian.org/med-team/augur/-/commit/f645e910276b5b6ed9116a19e4a22dec1c10f24f
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