Merge pull request #136 from MatthewRalston/stderr_logging_cleanup

Stderr logging - cleanup only

.clean_local_install.sh

@@ -19,7 +19,10 @@ EOF
 
 
 rm -rf /home/matt/.pyenv/versions/kdb/lib/python3.11/site-packages/kmerdb /home/matt/.pyenv/versions/kdb/lib/python3.11/site-packages/kmerdb-*.egg-info /home/matt/Projects/kdb/kmerdb.egg-info /home/matt/Projects/kdb/build /home/matt/Projects/kdb/dist
+
+rm -rf /home/matt/.pyenv/versions/kdb/lib/python3.12/site-packages/kmerdb /home/matt/.pyenv/versions/kdb/lib/python3.12/site-packages/kmerdb-*.egg-info
 rm -rf /home/matt/.pyenv/versions/3.11.7/envs/kdb/lib/python3.11/site-packages/kmerdb-*
+rm -rf /home/matt/.pyenv/versions/3.12.2/envs/kdb/lib/python3.12/site-packages/kmerdb-0.7.8.dist-info/
 cd /home/matt/Projects/kdb/
 rm -rf dist build kmerdb.egg-info wheelhouse
 cd

.deploy.md

@@ -0,0 +1,110 @@
+# Deployment
+
+Update pyproject.toml *with* the contents of requirements.txt
+
+
+Used the following to investigate whether or not the requirements are satsified globally.
+
+```
+# --prefix=your/.venv
+
+# TMPDIR=/your/choice
+
+
+# pip install --isolated 
+
+pip install --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache -r requirements.txt --dry-run
+
+#----------------------------------------
+# Build-chain
+pip install setuptools>=61.0 --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run
+pip install  wheel  --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run
+pip install numpy>=1.22.0  --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run
+#pip install build>=0.9.0?  --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run
+
+# Fixed #(? #3/31/24 also still out of wack, had been using a more modern toolchain for essentially no-reason. hold up)
+distlib>=0.3.8 # 3/31/24 -  May need downgrade due to setuptools, build, or distlib compatibility layers under pip
+Cython>=3.0.8 #?  3/31/24  - same issue. needlessly restrictive, some issues in build system prevent good correspondence with compatibility as either a conda toolchain/buildchain or a pypi module. still needs fix.
+
+
+pip install numpy>=1.26.3 --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run
+pip install numpy>=1.26.3 --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run
+
+# I think build and distlib are used for Cythonization of the Pearson correlation coefficient
+# I think setuptools is a Python PyPI compatibility layer for dependency layer.
+
+
+
+
+
+
+
+#----------------------------------------
+# module reqrmtx
+
+# biopython
+biopython>=1.81
+pip install numpy>=1.26.3 --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run
+
+# --------------- docutils
+docutils>=0.17
+#docutils==0.18.1
+pip install numpy>=1.26.3 --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run
+
+# # -------------- Sphinx
+# # 3/31/24 - May need a version bump
+sphinx>=4.3.2
+
+#sphinxcontrib-htmlhelp>=2.0.0
+#sphinxcontrib-serializinghtml>=1.1.5
+
+# # 3/31/24 - Also needs a version fix. This is live i think.
+#sphinx-rtd-theme>=1.0.0
+
+
+## Um hs do these all need version bumps
+
+
+# # Graphics
+
+pip install matplotlib>=3.8.2 --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run
+# # Scientific computing
+
+#########################################
+pip install numpy>=1.26.3 --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run
+pip install  pandas>=2.2.0  --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run
+
+
+#########################################
+# Configurations
+
+
+# gtfh
+# # 3/31/24 needs a downgrade too
+pip install PyYAML>=6.0.1 --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run
+pip install  jsonschema>=4.21.1  --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run
+
+
+
+psutil>=5.9.8
+pip install psutil>=5.9.8 --isolated -i https://pypi.org/simple --prefix .venv_cache --cache-dir $TMPDIR/.pip_cache --dry-run
+
+
+```
+
+
+
+
+
+###### 3/31/24
+
+
+## Version downgrades and optionals. 
+
+
+biopython
+1.8.3->1.81
+
+Testing alternate install/build system.
+
+## 

README.md

@@ -49,7 +49,7 @@ All other dependencies are managed directly by pip.
 ### OSX and Linux release:
 
 ```sh
-pip install kmerdb
+pip install --python-version 3.7.4 --pre kmerdb
 ```
 
 
@@ -58,7 +58,7 @@ pip install kmerdb
 
 ```sh
 git clone https://github.com/MatthewRalston/kmerdb.git
-pip install -e .
+pip install .
 ```
 
 ## Usage Example