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](pandas-dev/pandas@v1.0.1...v2.0.0)

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

Signed-off-by: dependabot[bot] <[email protected]>

* update lots of deps

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: C. Titus Brown <[email protected]>

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

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

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

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

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",
 )