Merge pull request #217 from smithlabcode/abismal-submodule-update

abismal submodule update
smithlabcode · Jun 2, 2024 · 5a1f5a6 · 5a1f5a6
2 parents bf1e6fe + 492ba2d
commit 5a1f5a6
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Showing 4 changed files with 6 additions and 7 deletions.
diff --git a/data/md5sum.txt b/data/md5sum.txt
@@ -16,7 +16,7 @@ bcbf01be810cbf4051292813eb6b9225  tests/tRex1.idx
 ec6a686617cad31e9f7a37a3d378e6ed  tests/two_epialleles.states
 93e38b20d162062a5d147c4290095a13  tests/mlml.out
 d947fe3d61ef7b1564558a69608f0e64  tests/methylome.pmd
-7d481d31e4316e97d519838f4887b10d  tests/reads.sam
-466e2715f0c677593e84b3790efbec6e  tests/reads.fmt.sam
-5583ebe1b689159f8eb0a93f32e2fd48  tests/reads.fmt.srt.uniq.sam
 d41d8cd98f00b204e9800998ecf8427e  tests/two_epialleles.amr
+7fff91916ffd22d4a934b74acf0c01a2  tests/reads.fmt.sam
+f963e689859dcf38a26acda9a65a6431  tests/reads.sam
+091eee8aa30193dafe9116120f72cec8  tests/reads.fmt.srt.uniq.sam
diff --git a/docs/content/environment.yaml b/docs/content/environment.yaml
@@ -1,3 +1,3 @@
 name: docs
 dependencies:
-  - jinja2<3.1.0
+  - Jinja2>3.1.4
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,8 +1,7 @@
-jinja2==3.0.3
+Jinja2>=3.1.4
 mkdocs>=1.3.1
 babel>=2.9.0
 click>=7.0
-Jinja2>=2.10.2
 Markdown>=3.2.1,<3.4
 PyYAML>=5.2
 watchdog>=2.0.0

diff --git a/src/abismal b/src/abismal
+38 −0		.github/ISSUE_TEMPLATE/bug_report.md
+20 −0		.github/ISSUE_TEMPLATE/feature_request.md
+4 −6		.github/workflows/macos-builds.yml
+3 −1		.github/workflows/ubuntu-builds.yml
+0 −39		Makefile
+7 −2		Makefile.am
+14 −2		configure.ac
+4 −4		data/md5sum.txt
+8 −9		src/AbismalAlign.hpp
+13 −13		src/AbismalIndex.cpp
+4 −0		src/AbismalIndex.hpp
+0 −75		src/Makefile
+1 −1		src/smithlab_cpp