Merge pull request #20 from timbernat/env-updates

Install + env updates

README.md

@@ -6,41 +6,64 @@ Polymer-Oriented LibrarY of Monomer Expression Rules and In-silico Synthesis Too
 
 A unified set of tools for monomer template generation, topology building, force-field parameterization, and MD simulations of general organic polymer systems within the OpenFF framework
 
-Source code for [Davel, Connor M., Bernat, Timotej, Wagner, Jeffrey R., and Shirts, Michael R., "Parameterization of General Organic Polymers within the Open Force Field Framework"](https://pubs.acs.org/doi/10.1021/acs.jcim.3c01691)
+Source code based upon concepts introduced in ["Parameterization of General Organic Polymers within the Open Force Field Framework" (Davel, Connor M., Bernat, Timotej, Wagner, Jeffrey R., and Shirts, Michael R.)](https://pubs.acs.org/doi/10.1021/acs.jcim.3c01691)
 
 ![abstract](docs/_static/polymer_param_graphic_TOC.png)
 
 
 ## Installation
 
-Currently, this package only supports a "dirty" developer install using conda/mamba and `pip`.  
-First, you will need to install the `conda` environment manager (either the lightweight [Miniconda Distribution](https://docs.anaconda.com/free/miniconda/miniconda-install/) (recommended) or the bulkier [Anaconda Distribution](https://www.anaconda.com/download)) if you don't already have it.
-Further, it is highly recommended (but optional) that you also have the `mamba` package manager installed (either through [Miniforge or Conda](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html)); this will greatly accelerate download times.  
+Currently, this package only supports a "dirty" `pip` installation from a clone of this GitHub repo.
+First, you will need to install some iteration of the `conda` environment manager. Possible builds (in decreasing order of recommendation) are:
+- The very-rapid `mamba` package manager; installable either through [Miniforge or Conda](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html)
+- The lightweight [Miniconda Distribution](https://docs.anaconda.com/free/miniconda/miniconda-install/)
+- The bulky [Anaconda Distribution](https://www.anaconda.com/download)
+Once you install one of these (or if you already have one installed on your system), you may proceed with on of the installation modes.
 
-Once `mamba` is installed, you can proceed with the dirty `polymerist` install into a safe virtual environment (named "polymerist-env" here).
+### 1) User Install
+
+For nominal use, `polymerist` can be installed into a safe virtual environment, named "polymerist-env" here.
 To install, execute the following set of commands in a command line interface (CLI) in whichever directory you'd like the dev installation to live:
+
+#### Mamba install:
 ```sh
 git clone https://github.com/timbernat/polymerist
 cd polymerist
-mamba env create -n polymerist-env -f devtools/conda-envs/polymerist-env.yml
+mamba env create -n polymerist-env -f devtools/conda-envs/release-build.yml
 mamba activate polymerist-env
-pip install -e .
+pip install .
 ```
 The third command will take **_at least_** a few minutes, and will make the CLI terminal quite busy; remain calm, that's normal!
 
+#### Vanilla Conda install:
 Equivalent commands using just `conda` (in case `mamba` has not been installed) are below. These will perform the same installation, just much more slowly:
 ```sh
 git clone https://github.com/timbernat/polymerist
 cd polymerist
-conda env create -n polymerist-env -f devtools/conda-envs/polymerist-env.yml
+conda env create -n polymerist-env -f devtools/conda-envs/release-build.yml
 conda activate polymerist-env
-pip install -e .
+pip install .
 ```
+
+### 1.1) OpenEye License
 As an optional last step, it is recommended that you correctly set up paths to your [OpenEye License](https://docs.eyesopen.com/toolkits/python/quickstart-python/license.html), if you have access to one.
 Portions of conformer-generation and partial-charge assignment in `polymerist` will work more effectively with the OpenEye toolkit installed and licensed, but 'polymerist' is set up to not require these closed-source dependencies.
 
 From here, you should be able to run `polymerist`-dependent scripts in the polymerist-env virtual environment active, either from the command line or from a [Jupyter Notebook](https://jupyter.org/)!
 
+### 2) Dev install
+
+Those developing for `polymerist` may like to have an editable local installation, in which they can make changes to the source code and test behavior changes in real-time.
+In this case, one requires an "editable build" which does **NOT** live in the site_packages dir of the created env. This type of installation proceeds as follows:
+```sh
+git clone https://github.com/timbernat/polymerist
+cd polymerist
+mamba env create -n polymerist-dev -f devtools/conda-envs/dev-build.yml
+mamba activate polymerist-dev
+pip install -e . --config-settings editable_mode=strict
+```
+The `--config-settings editable_mode` flag in the final line allows this install to "play nicely" with PyLance, making auto-completion and navigation to source code much easier for VSCode users.
+It is optional, and can be removed if this compatibility is not desired.
 
 ### Copyright
 

devtools/conda-envs/polymerist-env.yml → devtools/conda-envs/dev-build.yml

@@ -1,4 +1,4 @@
-name: polymerist-env
+name: polymerist-explicit
 channels:
   - openeye
   - conda-forge
@@ -12,6 +12,7 @@ dependencies:
   - ambertools=23.3=py311h9fea076_6
   - annotated-types=0.6.0=pyhd8ed1ab_0
   - anyio=4.3.0=pyhd8ed1ab_0
+  - anytree=2.12.1=pyhd8ed1ab_0
   - argon2-cffi=23.1.0=pyhd8ed1ab_0
   - argon2-cffi-bindings=21.2.0=py311h459d7ec_4
   - arpack=3.8.0=nompi_h0baa96a_101

devtools/conda-envs/polymerist-minimal.yml → devtools/conda-envs/release-build.yml

@@ -1,4 +1,4 @@
-name: polymerist-minimal
+name: polymerist-env
 channels:
     - conda-forge
     - openeye
@@ -13,6 +13,7 @@ dependencies:
     - pandas
     - dgl >=1.0
     - networkx
+    - anytree
 
     # MD engines
     - openmm
@@ -22,6 +23,7 @@ dependencies:
     # Molecule building
     - mbuild
     - rdkit
+    - openeye-toolkits # TODO: consider making this optional?
 
     # Visualization
     - pillow