From 71b187bb7e023f70592c5aa731c9448045f0536c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 10 Apr 2023 13:51:51 +0000
Subject: [PATCH] Update pandas, pytest, and sourmash requirements. (#275)

* Update pandas requirement from <2,>1 to >1,<3

Updates the requirements on [pandas](https://github.com/pandas-dev/pandas) to permit the latest version.
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Changelog](https://github.com/pandas-dev/pandas/blob/main/RELEASE.md)
- [Commits](https://github.com/pandas-dev/pandas/compare/v1.0.1...v2.0.0)

---
updated-dependencies:
- dependency-name: pandas
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* update lots of deps

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: C. Titus Brown <titus@idyll.org>
---
 environment.yml                     | 2 +-
 genome_grist/conf/env/papermill.yml | 4 ++--
 genome_grist/conf/env/sourmash.yml  | 2 +-
 setup.cfg                           | 4 ++--
 setup.py                            | 2 +-
 5 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/environment.yml b/environment.yml
index 824abeb..2917cc6 100644
--- a/environment.yml
+++ b/environment.yml
@@ -8,5 +8,5 @@ dependencies:
  - snakemake-minimal==7.25.0
  - click>=7,<9
  - lxml==4.9.2
- - pandas>1,<2
+ - pandas>1,<3
  - python>=3.7,<3.10
diff --git a/genome_grist/conf/env/papermill.yml b/genome_grist/conf/env/papermill.yml
index fa1af7a..24f72b7 100644
--- a/genome_grist/conf/env/papermill.yml
+++ b/genome_grist/conf/env/papermill.yml
@@ -9,6 +9,6 @@ dependencies:
     - ipykernel
     - matplotlib>=3.4.3,<4
     - numpy>=1.21.3,<2
-    - pandas>=1.3.4,<2
-    - sourmash>=4.6.1,<5
+    - pandas>=1.3.4,<3
+    - sourmash>=4.8.0,<5
     - python>=3.8,<3.10
diff --git a/genome_grist/conf/env/sourmash.yml b/genome_grist/conf/env/sourmash.yml
index 4fb32bc..8154708 100755
--- a/genome_grist/conf/env/sourmash.yml
+++ b/genome_grist/conf/env/sourmash.yml
@@ -5,7 +5,7 @@ channels:
 dependencies:
  - python>=3.8,<3.10
  - screed>=1.1,<2
- - sourmash>=4.6.1,<5
+ - sourmash>=4.8.0,<5
  - pip
  - pip:
    - git+https://github.com/dib-lab/genome-grist.git#egg=genome-grist
diff --git a/setup.cfg b/setup.cfg
index 337e2a6..a00ef63 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -6,7 +6,7 @@ addopts = --verbose
 
 [options.extras_require]
 test =
-    pytest>=5.1.2,<7.3.0
+    pytest>=5.1.2,<7.4.0
     pytest-cov
     pytest-dependency
-    sourmash>=4.6.1,<5
+    sourmash>=4.8.0,<5
diff --git a/setup.py b/setup.py
index 222879e..5ca1a4f 100644
--- a/setup.py
+++ b/setup.py
@@ -42,7 +42,7 @@
     tests_require=["pytest", "pytest-dependency==0.5.1"],
     use_scm_version={"write_to": "genome_grist/version.py"},
     install_requires=["snakemake==7.25.0", "click>=7,<9", "lxml==4.9.2",
-                      "pandas>1,<2"],
+                      "pandas>1,<3"],
     long_description=long_description,
     long_description_content_type="text/markdown",
 )