Merge branch 'localdev' into 'next'

Containerize the Remote-Worker Server

See merge request !14

.env

@@ -9,3 +9,15 @@ DJANGO_SUPERUSER_EMAIL=webreflect@localhost
 APP_SECRET='y&#94bnh&4zw3s)0h2&f$ve87_1c_t*+hxfl=2v9429^75-t03'
 SETTINGS_DIR=/var/www/web_reflectivity/app/web_reflectivity
 C_FORCE_ROOT=true
+###
+# Remote worker
+###
+TEST_USER_NAME=testuser
+TEST_USER_PASSWD=feg56PUV
+TEST_USER_EMAIL=tester@example.com
+# Valid options to choose are ('localhost', 'analysis.sns.gov')
+JOB_HANDLING_HOST=localhost
+JOB_HANDLING_PORT=22
+# Valid options to choose are ('/tmp', '~')
+REFL1D_JOB_DIR='/tmp'
+JOB_HANDLING_INTERPRETER='python'

cfg/worker/Dockerfile

+# latest miniconda3 image
+FROM continuumio/miniconda3
+
+ENV PYTHONUNBUFFERED 1
+ENV CFLAGS "-std=c++11"
+ENV LANG en_US.UTF-8
+ENV LANGUAGE en_US.UTF-8
+ENV LC_COLLATE C
+ENV LC_CTYPE en_US.UTF-8
+
+WORKDIR /opt/refl1d
+COPY . .
+
+# This line will throw error if using an old miniconda3 image.
+# To correct, one must build a miniconda3 image while piling all apt-get statements together into one
+# https://hub.docker.com/r/continuumio/miniconda3/dockerfile
+RUN apt-get update && apt-get install -y vim emacs iputils-ping net-tools openssh-client openssh-server
+
+RUN conda install --name base -c conda-forge mamba
+RUN mamba env update --name base --file environment.yml
+
+# Will start conda environment when $HOME/.bashrc is invoked
+RUN echo "source /etc/profile.d/conda.sh" >> /etc/skel/.bashrc
+RUN echo "conda activate base" >> /etc/skel/.bashrc
+
+# test installation
+RUN cd /tmp && git clone https://github.com/reflectometry/refl1d.git && cd refl1d/  && git checkout tags/v0.8.15
+RUN cd /tmp/refl1d/ && pytest ./tests
+
+CMD ["/bin/bash"]

cfg/worker/docker-entrypoint.sh

+#!/bin/bash
+set -e  # stop and exit script if any command or pipeline returns
+
+# crate account for test user
+useradd -m -p $(openssl passwd -crypt ${TEST_USER_PASSWD}) -s /bin/bash -G users ${TEST_USER_NAME}
+
+# start the ssh daemon
+/etc/init.d/ssh start
+
+# hack preventing container from exiting
+tail -f /dev/null

cfg/worker/environment.yml

+name: refl1d
+channels:
+  - conda-forge
+dependencies:
+  - python=3.8
+  - pip
+  - cython
+  - numpy
+  - scipy
+  - matplotlib
+  - wxpython
+  - git
+  - pytest
+  - pytest-cov
+  - pip:
+    - refl1d==0.8.15

dev-docs/a_manual_fit.rst

+====================
+A Manual Fit Session
+====================
+
+This page describes the steps one takes when fitting 1D reflectivity data on the web application, starting at
+the point when one logs in the application.
+
+After login in, click in `Choose File` in order to select file `double_layer.txt` found in directory `test/data/`. After
+selecting the file, click in `Submit` in order to upload the file. The file will show up in the list of uploaded files.
+
+.. image:: images/a_manual_fit_1.png
+    :width: 800px
+    :align: center
+    :alt: file double_later.txt uploaded
+
+Click in the link `click to fit`. A default initial layer structure will be shown near the bottom of the model page:
+
+.. image:: images/a_manual_fit_2.png
+    :width: 800px
+    :align: center
+    :alt: default layer structure
+
+The default layer structure has only one layer, limited by air and Si on both sides. The solution layer structure
+contains two layers with specific thickness and other properties, namely
+
+.. image:: images/a_manual_fit_3.png
+    :width: 800px
+    :align: center
+    :alt: solution layer structure
+
+Thus, we must include an additional layer into the default initial layer structure. We use the "+" button for that
+(in the below picture, enclosed in the dashed-line red circle). However, before adding a layer we must evaluate
+or fit the current model. Press on the `Evaluate` button (in the below picture, enclosed in the dashed-line
+purple circle)
+
+.. image:: images/a_manual_fit_4.png
+    :width: 800px
+    :align: center
+    :alt: evaluating the model
+
+The evaluation prints the current model curve on top of the data. The plot is located near the top of the model page.
+As one would expect, the initial model is a poor fit of the data:
+
+.. image:: images/a_manual_fit_5.png
+    :width: 800px
+    :align: center
+    :alt: a poor fit
+
+The poor fit is of little consequence now. Let's click in the "+" button now to add a new layer. This is the current
+model with two layers:
+
+.. image:: images/a_manual_fit_6.png
+    :width: 800px
+    :align: center
+    :alt: two-layer bad model
+
+We enter the parameters of the solution layer structure into the model:
+
+.. image:: images/a_manual_fit_7.png
+    :width: 800px
+    :align: center
+    :alt: solution entered
+
+This should provide a model curve closely fitting the data. We're going to create an initial guess for the fit
+starting with these optimal parameters. We just distort the two thickness parameters for layers A and B. The goal is
+to recover the solution thickness when we fit the model. In this case we entered initial values of 500 and 40
+Angstroms for layers `A` and `B`, respectively (red circle in the below picture). Also, we removed the nearby
+checkmarks, indicating these are fit parameters (purple circle in the below picture). When a parameter is unchecked,
+a `min` and `max` range becomes available (range rectangle in the below picture). We have adjusted the ranges so
+that our initial guesses fall right in the middle of the ranges:
+
+.. image:: images/a_manual_fit_8.png
+    :width: 800px
+    :align: center
+    :alt: initial guess
+
+Click the `Evaluate` button to see how our initial guess aligns with the data. We find an "out-of-phase" fit:
+
+.. image:: images/a_manual_fit_9.png
+    :width: 800px
+    :align: center
+    :alt: out-of-phase fit
+
+We now fit the model by clicking in the `Fit` button. The job is submitted to the (local or remote) work server
+and fits results will be available once the fit job is finished. A message at the top of the page indicates
+this is so, with a link to display the fit:
+
+.. image:: images/a_manual_fit_10.png
+    :width: 200px
+    :align: center
+    :alt: fit results are ready
+
+After clicking in the link, we can inspect the fit to the data and the fit parameters
+
+.. image:: images/a_manual_fit_11.png
+    :width: 800px
+    :align: center
+    :alt: fitted curve
+
+.. image:: images/a_manual_fit_12.png
+    :width: 800px
+    :align: center
+    :alt: fitted parameters
+
+We obtain thicknesses `578.3` and `42.89` (compare to given solution parameters `577.6` and `44.75`).
+
+If so desired, we can save the fit by clicking in the `save model` link (red circle in the below picture):
+
+.. image:: images/a_manual_fit_13.png
+    :width: 800px
+    :align: center
+    :alt: save model
+
+A pop-up will confirm the model was saved:
+
+.. image:: images/a_manual_fit_14.png
+    :width: 200px
+    :align: center
+    :alt: confirmation of model saved
+
+Close the pop-up by clicking in the `OK` button. Then, click in the `show models` button (red circle in the below
+picture):
+
+.. image:: images/a_manual_fit_15.png
+    :width: 800px
+    :align: center
+    :alt: confirmation of model saved
+
+The model will show at the top of the list of available models:
+
+.. image:: images/a_manual_fit_16.png
+    :width: 800px
+    :align: center
+    :alt: list of available models
+
+Clicking in the pencil button (red circle in the picture above) will show the fit parameters:
+
+.. image:: images/a_manual_fit_17.png
+    :width: 500px
+    :align: center
+    :alt: fit parameters for the selected saved model
+
+This finishes the manual fit session!