Merge pull request petrobras#31 from petrobras/other_improvements

Replace requirements.txt with environment.yml
CCT-Sep-2022-AI-Group-1 · Sep 28, 2022 · a4a50c6 · a4a50c6
2 parents 7a613bc + 09eb439
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diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -85,9 +85,8 @@ At level 2, the 3W toolkit is implemented in sub-modules as discribed [here](3W_
 
 ## Executing examples
 
-Before executing examples of how to use the 3W toolkit available in this repository, we 
-recommend that you set up a Python Virtual Environment with the packages versions listed in the [requirements.txt](requirements.txt). This file is generated automatically with the [pipreqs](https://pypi.org/project/pipreqs/).
-
+To execute examples of how to use the 3W toolkit available in this repository, see the instructions related to [reproducibility](README.md#reproducibility).
+
 # Proposing contributions
 
 For each type of expected contribution, there is a subsection below with specific instructions. The last subsection specifies additional requirements for contributions to be incorporated into this project.

diff --git a/README.md b/README.md
@@ -122,4 +122,25 @@ The list below with examples of how to use the 3W toolkit will be incremented th
 * Binary classifier of Spurious Closure of DHSV:
   * [Baseline](problems/01_binary_classifier_of_spurious_closure_of_dhsv/_baseline/main.ipynb)
 
-For a contribution of yours to be listed here, follow the instructions detailed in the [CONTRIBUTING GUIDE](CONTRIBUTING.md).
+For a contribution of yours to be listed here, follow the instructions detailed in the [CONTRIBUTING GUIDE](CONTRIBUTING.md).
+
+## Reproducibility
+
+For all results generated by the 3W toolkit to be consistent, we recommend you create and use a virtual environment with the packages versions specified in the [environment.yml](environment.yml), which was generated with [conda](https://docs.conda.io). First you have to install the [Anaconda](https://anaconda.org/). Then open an Anaconda Prompt, make sure the current directory is the directory where you have the 3W and run the following commands as needed:
+
+* To create a virtual environment from our [environment.yml](environment.yml): 
+```
+$ conda env create -f environment.yml
+```
+* To activate the created virtual environment:
+```
+$ conda activate 3w
+```
+* To use the 3W toolkit resources interactively:
+```
+$ python
+```
+* To initialize a local Jupyter Notebook server:
+```
+$ jupyter notebook
+```
diff --git a/environment.yml b/environment.yml
@@ -0,0 +1,183 @@
+name: 3w
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - argon2-cffi=21.3.0=pyhd8ed1ab_0
+  - argon2-cffi-bindings=21.2.0=py310he2412df_2
+  - asttokens=2.0.8=pyhd8ed1ab_0
+  - attrs=22.1.0=pyh71513ae_1
+  - backcall=0.2.0=pyh9f0ad1d_0
+  - backports=1.0=py_2
+  - backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
+  - beautifulsoup4=4.11.1=pyha770c72_0
+  - bleach=5.0.1=pyhd8ed1ab_0
+  - brotli=1.0.9=h8ffe710_7
+  - brotli-bin=1.0.9=h8ffe710_7
+  - bzip2=1.0.8=h8ffe710_4
+  - ca-certificates=2022.9.24=h5b45459_0
+  - certifi=2022.9.24=pyhd8ed1ab_0
+  - cffi=1.15.1=py310hcbf9ad4_0
+  - colorama=0.4.5=pyhd8ed1ab_0
+  - contourpy=1.0.5=py310h232114e_0
+  - cycler=0.11.0=pyhd8ed1ab_0
+  - debugpy=1.6.3=py310h8a704f9_0
+  - decorator=5.1.1=pyhd8ed1ab_0
+  - defusedxml=0.7.1=pyhd8ed1ab_0
+  - entrypoints=0.4=pyhd8ed1ab_0
+  - executing=1.1.0=pyhd8ed1ab_0
+  - flit-core=3.7.1=pyhd8ed1ab_0
+  - fonttools=4.37.3=py310h8d17308_0
+  - freetype=2.12.1=h546665d_0
+  - gettext=0.19.8.1=h5728263_1009
+  - glib=2.74.0=h12be248_0
+  - glib-tools=2.74.0=h12be248_0
+  - gst-plugins-base=1.20.3=h001b923_2
+  - gstreamer=1.20.3=h6b5321d_2
+  - icu=70.1=h0e60522_0
+  - importlib-metadata=4.11.4=py310h5588dad_0
+  - importlib_resources=5.9.0=pyhd8ed1ab_0
+  - intel-openmp=2022.1.0=h57928b3_3787
+  - ipykernel=6.16.0=pyh025b116_0
+  - ipython=8.5.0=pyh08f2357_1
+  - ipython_genutils=0.2.0=py_1
+  - ipywidgets=8.0.2=pyhd8ed1ab_1
+  - jedi=0.18.1=pyhd8ed1ab_2
+  - jinja2=3.1.2=pyhd8ed1ab_1
+  - joblib=1.2.0=pyhd8ed1ab_0
+  - jpeg=9e=h8ffe710_2
+  - jsonschema=4.16.0=pyhd8ed1ab_0
+  - jupyter=1.0.0=py310h5588dad_7
+  - jupyter_client=7.3.5=pyhd8ed1ab_0
+  - jupyter_console=6.4.4=pyhd8ed1ab_0
+  - jupyter_core=4.11.1=py310h5588dad_0
+  - jupyterlab_pygments=0.2.2=pyhd8ed1ab_0
+  - jupyterlab_widgets=3.0.3=pyhd8ed1ab_0
+  - kiwisolver=1.4.4=py310h476a331_0
+  - krb5=1.19.3=h1176d77_0
+  - lcms2=2.12=h2a16943_0
+  - lerc=4.0.0=h63175ca_0
+  - libblas=3.9.0=16_win64_mkl
+  - libbrotlicommon=1.0.9=h8ffe710_7
+  - libbrotlidec=1.0.9=h8ffe710_7
+  - libbrotlienc=1.0.9=h8ffe710_7
+  - libcblas=3.9.0=16_win64_mkl
+  - libclang=14.0.6=default_hf4acfee_0
+  - libclang13=14.0.6=default_h8992b79_0
+  - libdeflate=1.14=hcfcfb64_0
+  - libffi=3.4.2=h8ffe710_5
+  - libglib=2.74.0=h79619a9_0
+  - libiconv=1.17=h8ffe710_0
+  - liblapack=3.9.0=16_win64_mkl
+  - libogg=1.3.4=h8ffe710_1
+  - libpng=1.6.38=h19919ed_0
+  - libsodium=1.0.18=h8d14728_1
+  - libsqlite=3.39.3=hcfcfb64_0
+  - libtiff=4.4.0=h8e97e67_4
+  - libvorbis=1.3.7=h0e60522_0
+  - libwebp-base=1.2.4=h8ffe710_0
+  - libxcb=1.13=hcd874cb_1004
+  - libxml2=2.10.2=h99b13fb_1
+  - libxslt=1.1.35=h34f844d_0
+  - libzlib=1.2.12=hcfcfb64_3
+  - lxml=4.9.1=py310he2412df_0
+  - m2w64-gcc-libgfortran=5.3.0=6
+  - m2w64-gcc-libs=5.3.0=7
+  - m2w64-gcc-libs-core=5.3.0=7
+  - m2w64-gmp=6.1.0=2
+  - m2w64-libwinpthread-git=5.0.0.4634.697f757=2
+  - markupsafe=2.1.1=py310he2412df_1
+  - matplotlib-base=3.6.0=py310h51140c5_0
+  - matplotlib-inline=0.1.6=pyhd8ed1ab_0
+  - mistune=2.0.4=pyhd8ed1ab_0
+  - mkl=2022.1.0=h6a75c08_874
+  - msys2-conda-epoch=20160418=1
+  - munkres=1.1.4=pyh9f0ad1d_0
+  - natsort=8.2.0=pyhd8ed1ab_0
+  - nbclient=0.6.8=pyhd8ed1ab_0
+  - nbconvert=7.0.0=pyhd8ed1ab_0
+  - nbconvert-core=7.0.0=pyhd8ed1ab_0
+  - nbconvert-pandoc=7.0.0=pyhd8ed1ab_0
+  - nbformat=5.6.1=pyhd8ed1ab_0
+  - nest-asyncio=1.5.5=pyhd8ed1ab_0
+  - notebook=6.4.12=pyha770c72_0
+  - numpy=1.23.3=py310h4a8f9c9_0
+  - openjpeg=2.5.0=hc9384bd_1
+  - openssl=1.1.1q=h8ffe710_0
+  - packaging=21.3=pyhd8ed1ab_0
+  - pandas=1.5.0=py310h1c4a608_0
+  - pandoc=2.19.2=h57928b3_0
+  - pandocfilters=1.5.0=pyhd8ed1ab_0
+  - parso=0.8.3=pyhd8ed1ab_0
+  - patsy=0.5.2=pyhd8ed1ab_0
+  - pcre2=10.37=hdfff0fc_1
+  - pickleshare=0.7.5=py_1003
+  - pillow=9.2.0=py310h52929f7_2
+  - pip=22.2.2=pyhd8ed1ab_0
+  - pkgutil-resolve-name=1.3.10=pyhd8ed1ab_0
+  - ply=3.11=py_1
+  - prometheus_client=0.14.1=pyhd8ed1ab_0
+  - prompt-toolkit=3.0.31=pyha770c72_0
+  - prompt_toolkit=3.0.31=hd8ed1ab_0
+  - psutil=5.9.2=py310h8d17308_0
+  - pthread-stubs=0.4=hcd874cb_1001
+  - pure_eval=0.2.2=pyhd8ed1ab_0
+  - pycparser=2.21=pyhd8ed1ab_0
+  - pygments=2.13.0=pyhd8ed1ab_0
+  - pyparsing=3.0.9=pyhd8ed1ab_0
+  - pyqt=5.15.7=py310hbabf5d4_0
+  - pyqt5-sip=12.11.0=py310h8a704f9_0
+  - pyrsistent=0.18.1=py310he2412df_1
+  - python=3.10.6=h9a09f29_0_cpython
+  - python-dateutil=2.8.2=pyhd8ed1ab_0
+  - python-fastjsonschema=2.16.2=pyhd8ed1ab_0
+  - python_abi=3.10=2_cp310
+  - pytz=2022.2.1=pyhd8ed1ab_0
+  - pywin32=303=py310he2412df_0
+  - pywinpty=2.0.8=py310h00ffb61_0
+  - pyzmq=24.0.1=py310hcd737a0_0
+  - qt-main=5.15.6=hf0cf448_0
+  - qtconsole=5.3.2=pyhd8ed1ab_0
+  - qtconsole-base=5.3.2=pyha770c72_0
+  - qtpy=2.2.0=pyhd8ed1ab_0
+  - scikit-learn=1.1.2=py310h3a564e9_0
+  - scipy=1.9.1=py310h578b7cb_0
+  - seaborn=0.12.0=hd8ed1ab_0
+  - seaborn-base=0.12.0=pyhd8ed1ab_0
+  - send2trash=1.8.0=pyhd8ed1ab_0
+  - setuptools=65.4.0=pyhd8ed1ab_0
+  - sip=6.6.2=py310h8a704f9_0
+  - six=1.16.0=pyh6c4a22f_0
+  - soupsieve=2.3.2.post1=pyhd8ed1ab_0
+  - stack_data=0.5.1=pyhd8ed1ab_0
+  - statsmodels=0.13.2=py310h2873277_0
+  - tbb=2021.6.0=h91493d7_0
+  - terminado=0.15.0=py310h5588dad_0
+  - threadpoolctl=3.1.0=pyh8a188c0_0
+  - tinycss2=1.1.1=pyhd8ed1ab_0
+  - tk=8.6.12=h8ffe710_0
+  - toml=0.10.2=pyhd8ed1ab_0
+  - tornado=6.2=py310he2412df_0
+  - traitlets=5.4.0=pyhd8ed1ab_0
+  - typing_extensions=4.3.0=pyha770c72_0
+  - tzdata=2022d=h191b570_0
+  - ucrt=10.0.20348.0=h57928b3_0
+  - unicodedata2=14.0.0=py310he2412df_1
+  - vc=14.2=hb210afc_7
+  - vs2015_runtime=14.29.30139=h890b9b1_7
+  - wcwidth=0.2.5=pyh9f0ad1d_2
+  - webencodings=0.5.1=py_1
+  - wheel=0.37.1=pyhd8ed1ab_0
+  - widgetsnbextension=4.0.3=pyhd8ed1ab_0
+  - winpty=0.4.3=4
+  - xorg-libxau=1.0.9=hcd874cb_0
+  - xorg-libxdmcp=1.1.3=hcd874cb_0
+  - xz=5.2.6=h8d14728_0
+  - zeromq=4.3.4=h0e60522_1
+  - zipp=3.8.1=pyhd8ed1ab_0
+  - zlib=1.2.12=hcfcfb64_3
+  - zstd=1.5.2=h7755175_4
+  - pip:
+    - about-time==3.1.1
+    - alive-progress==2.4.1
+    - grapheme==0.6.0