update deps

README.md

@@ -123,12 +123,14 @@ dependencies via [Conda][conda]:
 git clone https://github.com/zavolanlab/htsinfer
 cd htsinfer
 conda env create --file environment.yml
-conda env update --file environment-dev.yml  # optional: install development/testing dependencies
+# Alternatively, to install with development dependencies,
+# run the following instead
+conda env create --file environment-dev.yml
 ```
 
-Note that creating the environment takes non-trivial time and it is strongly
-recommended that you install [Mamba][mamba] and replace `conda` with `mamba`
-in the previous commands.
+> Note that creating the environment takes non-trivial time and it is strongly
+> recommended that you install [Mamba][mamba] and replace `conda` with `mamba`
+> in the previous command.
 
 Then, activate the `htsinfer` Conda environment with:
 

environment-dev.yml

@@ -1,11 +1,25 @@
 name: htsinfer
 channels:
+  - bioconda
+  - conda-forge
   - defaults
 dependencies:
+  - biopython>=1.78
   - coverage>=5.3
+  - cutadapt>=3.5, <=4.2
   - flake8>=3.8.4
+  - kallisto>=0.46.1, <= 0.48.0
   - mypy>=0.782
+  - numpy >=1.22, <1.25
+  - pandas >=1.3.5, <1.4.0
+  - pip>=20.2.3
+  - pyahocorasick>=1.4.0
+  - pydantic>=1.8.1, <2
   - pylint>=2.4.4
+  - pysam>=0.16.0
   - pytest>=6.1.0
+  - python>3.6, <3.10
+  - star>=2.7.6
   - pip:
     - python-semantic-release>=7.15.0
+    - -e .

environment.yml

@@ -1,12 +1,13 @@
 name: htsinfer
 channels:
-  - defaults
   - bioconda
   - conda-forge
+  - defaults
 dependencies:
   - biopython>=1.78
   - kallisto>=0.46.1, <= 0.48.0
-  - pandas>=1.0.5
+  - numpy >=1.22, <1.25
+  - pandas >=1.3.5, <1.4.0
   - pip>=20.2.3
   - pyahocorasick>=1.4.0
   - pydantic>=1.8.1, <2