feat: add contribution guide and CoC (OpenBioML#6)

.github/workflows/install.yaml

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+# GitHub action that attempts to install the conda env
+# from conda.yaml
+# then run black, isort, flake8
+
+name: Install
+on: [push, pull_request]
+jobs:
+  install:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          environment-file: conda.yaml
+          activate-environment: chemnlp
+          python-version: 3.7
+          auto-update-conda: true
+          auto-activate-base: false
+      - name: Install
+        run: |
+          conda env create -f conda.yml 
+          conda activate chemnlp
+      - name: Lint
+        run: |
+          conda activate chemnlp
+          black --check .
+          isort --check-only .
+          flake8 .

CONTRIBUTING.md

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+There are many different ways to contribute to ChemNLP! 
+You can get in touch via the GitHub [task board](https://github.com/orgs/OpenBioML/projects/5?query=is:open+sort:updated-desc) and [issues](https://github.com/OpenBioML/chemnlp/issues?q=is:issue+is:open+sort:updated-desc&query=is:open+sort:updated-desc) and our [Discord](https://t.co/YMzpevmkiN).
+
+## Pre-Requisites
+Please make a [GitHub account](https://github.com/) prior to implementing a dataset; you can follow instructions to install git [here](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git).
+
+1. [Fork](https://docs.github.com/en/get-started/quickstart/fork-a-repo) the [ChemNLP repository](https://github.com/OpenBioML/chemnlp)
+2. [Clone the you fork](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository)
+3. [Make a new branch](https://git-scm.com/book/en/v2/Git-Branching-Basic-Branching-and-Merging)
+4. Please try using [conventional commits](https://www.conventionalcommits.org/en/v1.0.0/) for formatting your commit messages
+
+## Create a development environment (For code/dataset contributions)
+
+For code and data contributions, we recommend you creata a [conda environment](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html). If you do not have conda already installed on your system, we recommend installing [miniconda](https://docs.conda.io/en/latest/miniconda.html):
+
+```bash
+conda env create -f conda.yml  # Creates a conda env
+conda activate chemnlp  # Activate your conda environment
+```
+
+# Implementing a dataset 
+
+## Contributing a dataset 
+One of the most important ways to contribute to the ChemNLP efforts is to implement a dataset. 
+With "implementing" we mean the following: 
+
+- Take a dataset from our [awesome list](https://github.com/kjappelbaum/awesome-chemistry-datasets) (if it is not there, please add it there first, so we keep track)
+- Make an issue in this repository that you want to add this dataset (we will label this issue and assign it to you)
+- Make a PR that adds in a new folder in `data`
+  - `meta.yaml` describing the dataset 
+  - `transform.py` Python code that transforms the original dataset (linked in `meta.yaml`) into a form that can be consumed by the loader
+  - If you need additional dependencies, 
+
+
+
+The `meta.yaml` has the following structure:
+
+```yaml
+name: aquasoldb # unique identifier, we will also use this for directory names
+description: | # short description what this dataset is about
+  Curation of nine open source datasets on aqueous solubility.
+  The authors also assigned reliability groups.
+targets:
+  - id: Solubility # name of the column in a tabular dataset
+    description: Experimental aqueous solubility value (LogS) # description of what this column means
+    units: log(mol/L) # units of the values in this column (leave empty if unitless)
+    type: continuous # can be "categorical", "ordinal", "continuous"
+    names: # names for the property (to sample from for building the prompts)
+      - solubility
+      - water solubility
+  - id: SD
+    description: Standard deviation of the experimental aqueous solubility value for multiple occurences
+    units: log(mol/L)
+    type: continuous
+    names:
+      - solubility
+      - water solubility
+      - solubility in water
+identifiers:
+  - id: InChI # column name
+    type: InChI # can be "SMILES", "SELFIES", "IUPAC", "OTHER"
+    description: International Chemical Identifier # description (optional, except for "OTHER")
+license: CC0 1.0 # license under which the original dataset was published
+num_points: 10000 # number of datapoints in this dataset
+links: # list of relevant links (original dataset, other uses, etc.)
+  - name: dataset
+    url: https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/OVHAW8
+    description: Original dataset
+bibtex: # citation(s) for this dataset in BibTeX format
+  - |
+    "@article{Sorkun_2019,
+    doi = {10.1038/s41597-019-0151-1},
+    url = {https://doi.org/10.1038%2Fs41597-019-0151-1},
+    year = 2019,
+    month = {aug},
+    publisher = {Springer Science and Business Media {LLC}},
+    volume = {6},
+    number = {1},
+    author = {Murat Cihan Sorkun and Abhishek Khetan and Süleyman Er},
+    title = {{AqSolDB}, a curated reference set of aqueous solubility and 2D descriptors for a diverse set of compounds},
+    journal = {Sci Data}
+    }"
+```
+
+For the typical material-property datasets, we will later use the `identifier` and `property` columns to create and fill prompt templates. 
+In case your dataset isn't a simple tabular dataset with chemical compounds and properties, please also add the following additional fields for the templates:
+
+
+```yaml
+templates:
+  - prompt: "Please answer the following chemistry question.\nDerive for the molecule with the <molecule_text> <molecule> the <expt_value_text>."
+    completion: "<exp_value>"
+  - prompt: "Please answer the following question.\nPredict the <expt_value_text> for <molecule>."
+    completion: "<exp_value>"
+fields:
+  exp_value:
+    values:
+      - name: exp_value
+        column: exp_value
+        text: adsorption energy
+      - name: calc_value
+        column: calc_value
+        text: adsorption free energy
+  molecule:
+    values:
+      - name: smiles
+        column: smiles
+        text:
+      - name: smiles
+        column: smiles
+        text: SMILES
+```
+
+This templating syntax should allow for quite some flexibility: For every template field we will look for the key, e.g., `exp_value` as well as `exp_value_text` (which can be used to describe to the field type/value).
+If this (`text`) is a column name, we will use the values from the column (therefore, effectively, jointly sample the `column` and `text` columns).
+If there are multiple values for one field, we will sample combinations. 
+If you want to suggest sampling from different prompt prefixes, you can do so by specifying a template fields and different `text` (but no `column`).
+
+## Implementing a dataloader
+
+TBD. 
+
+
+## Implementing tokenizers 
+
+TBD.
+

README.md

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-# chemnlp
+[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](code_of_conduct.md)
+
+# ChemNLP
 ChemNLP project

code_of_conduct.md

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+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[INSERT CONTACT METHOD].
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations

conda.yaml

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+name: chemnlp
+dependencies:
+  - python>=3.7
+  - pip
+  - pip:
+      - -r dev-requirements.txt
+      - -r requirements.txt

dev-requirements.txt

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+black>=22.1.0,<22.2.0
+flake8>=3.8.3,<3.9.0
+isort>=5.0.0,<5.1.0

requirements.txt

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+datasets>=2.8.0,<3.0.0
+numpy>=1.21.2
+openpyxl>=3.0.9,<3.1.0
+pandas>=1.3.3