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608721b
Bind with CrysFML
AndrewSazonov Oct 13, 2020
158c2ae
Fix python to be 3.7
AndrewSazonov Oct 13, 2020
fa00a93
Add test action
AndrewSazonov Oct 13, 2020
8a8d842
Disable CFML
AndrewSazonov Oct 13, 2020
a9e441a
Set up access to private repos
AndrewSazonov Oct 13, 2020
3115bda
Try CI
AndrewSazonov Oct 13, 2020
a338b1a
Print some debug info
AndrewSazonov Oct 13, 2020
d9227fe
Disable automatic creation of virtualenvs
AndrewSazonov Oct 13, 2020
a520b78
Up
AndrewSazonov Oct 13, 2020
6f532c3
Set up PYTHONPATH
AndrewSazonov Oct 13, 2020
f0eddf6
Print some more debug info
AndrewSazonov Oct 13, 2020
b26d65f
Up
AndrewSazonov Oct 13, 2020
77d7105
Up
AndrewSazonov Oct 13, 2020
2b77a08
Install python manually
AndrewSazonov Oct 13, 2020
3b6d633
Seeding code
wardsimon Oct 14, 2020
69ae382
Merge remote-tracking branch 'origin/DAS-271' into DAS-271
wardsimon Oct 14, 2020
7f4d473
Fix adding phase to sample
wardsimon Oct 14, 2020
7866685
Support for multi-phases
wardsimon Oct 16, 2020
3898407
Modify interface for multiphase
AndrewSazonov Oct 16, 2020
95e64c7
Merge remote-tracking branch 'origin/DAS-271' into DAS-271
AndrewSazonov Oct 16, 2020
b416b17
Add ability to select phase for output
wardsimon Oct 16, 2020
89e5bb5
Merge remote-tracking branch 'origin/DAS-271' into DAS-271
wardsimon Oct 16, 2020
88e7446
First implementation of cryspy
wardsimon Oct 17, 2020
6cddb49
Update sample
wardsimon Oct 19, 2020
88c7914
Fixup naming conventions
wardsimon Oct 19, 2020
c55b9c2
Recursive path gen update
wardsimon Oct 19, 2020
ee88c96
Add debuging
wardsimon Oct 19, 2020
dae6b99
Add a Jupyter notebook
wardsimon Oct 19, 2020
5bf362c
Create devcontainer.json
wardsimon Oct 19, 2020
6f24128
Create Dockerfile
wardsimon Oct 19, 2020
24b2f5d
Update devcontainer.json
wardsimon Oct 19, 2020
e2dee45
Update devcontainer.json
wardsimon Oct 19, 2020
5058690
Update devcontainer.json
wardsimon Oct 19, 2020
e9a558f
Create Base.Dockerfile
wardsimon Oct 19, 2020
218a219
Create common-debian.sh
wardsimon Oct 19, 2020
210fce9
Create python-debian.sh
wardsimon Oct 19, 2020
b1767ad
Create node-debian.sh
wardsimon Oct 19, 2020
d3a1479
Change the way phases are managed
wardsimon Oct 21, 2020
3081014
Modify formation of Pattern
wardsimon Oct 21, 2020
0dec13a
Remove monty
AndrewSazonov Oct 22, 2020
0581108
Update example notebook
wardsimon Oct 23, 2020
2f6c5e2
Rename Cryspy -> CrysPy
AndrewSazonov Oct 23, 2020
2e46f22
Change from cryspy -> CrysPy
wardsimon Oct 23, 2020
7425f85
Introduce a fitting example
wardsimon Oct 23, 2020
04c3107
Initial implementation of GSAS-II
AndrewSazonov Oct 26, 2020
02bc71c
Load GSASII from github (macOS only)
AndrewSazonov Oct 27, 2020
06d9e57
Import GSASII
AndrewSazonov Oct 27, 2020
9187c58
Use CFML so_macos branch
AndrewSazonov Oct 27, 2020
7e7d26a
fix branch name
AndrewSazonov Oct 27, 2020
6a30094
Update import GSASII
AndrewSazonov Oct 27, 2020
9072c1e
fix platform call
AndrewSazonov Oct 27, 2020
846b2e1
Set matplotlib version
AndrewSazonov Oct 27, 2020
b3a2c59
try matplotlib 3.2.2
AndrewSazonov Oct 27, 2020
e63a6f6
Delete poetry.lock
AndrewSazonov Oct 27, 2020
307e478
Refactor gsas
AndrewSazonov Oct 28, 2020
75a7aa2
Make CrysPy default calc
AndrewSazonov Oct 28, 2020
0ba9a0e
Read/write temp files from default temp dir
AndrewSazonov Oct 28, 2020
a4c62dd
Use poetry update in CI
AndrewSazonov Oct 28, 2020
bbd66a6
Add libs to dependencies
AndrewSazonov Oct 28, 2020
f94ed81
Fix import GSAS
AndrewSazonov Oct 28, 2020
24333df
Update init
AndrewSazonov Oct 28, 2020
c7a3160
Print location of Python dylib
AndrewSazonov Nov 4, 2020
c3f389e
Try default github python
AndrewSazonov Nov 4, 2020
7d2f5a7
Update test.yml
AndrewSazonov Nov 4, 2020
2c5cb73
Update test.yml
AndrewSazonov Nov 4, 2020
88b2014
Update test.yml
AndrewSazonov Nov 4, 2020
4528174
Relink CrysFML from default Python dylib
AndrewSazonov Nov 4, 2020
a655579
Update test.yml
AndrewSazonov Nov 4, 2020
405c5ae
Update test.yml
AndrewSazonov Nov 4, 2020
efcff07
Fix path to CFML so
AndrewSazonov Nov 4, 2020
f22d33b
Update test.yml
AndrewSazonov Nov 4, 2020
410a96f
Try on ubuntu
AndrewSazonov Nov 4, 2020
04f7906
Fix path to CFML so
AndrewSazonov Nov 4, 2020
6e1a4b0
Fix matrix.os name
AndrewSazonov Nov 4, 2020
90a7366
Fix path for patchelf
AndrewSazonov Nov 4, 2020
ffe3dc4
Try script for relinking crysfml
AndrewSazonov Nov 4, 2020
b453c53
Try on ubuntu
AndrewSazonov Nov 4, 2020
c4cb322
Show some debug info
AndrewSazonov Nov 4, 2020
c7bf333
Update temp cif printing
AndrewSazonov Nov 5, 2020
3bae5bb
Update __init__.py
AndrewSazonov Nov 6, 2020
5e00682
Update test.yml
AndrewSazonov Nov 6, 2020
b4a6f88
New crysfml api
AndrewSazonov Nov 6, 2020
5712fb5
New cfml api
AndrewSazonov Nov 9, 2020
be31a01
Remove old CMFL_api
AndrewSazonov Nov 9, 2020
4249b47
Update to gsas
AndrewSazonov Nov 9, 2020
fd90bd9
Update relink cryspy script
AndrewSazonov Nov 9, 2020
1fb6487
Fix CFML path
AndrewSazonov Nov 9, 2020
222957d
Test CI on macos and ubuntu
AndrewSazonov Nov 9, 2020
c7c4117
Fix ci script
AndrewSazonov Nov 9, 2020
898bb8c
Add Point based background logic
wardsimon Nov 16, 2020
e35323d
Add zero_shift parameter
AndrewSazonov Nov 16, 2020
5fbce61
More BG work
wardsimon Nov 16, 2020
f3e535d
Update background label
AndrewSazonov Nov 16, 2020
c22dd18
Sorted backgrounds
wardsimon Nov 16, 2020
a413ae8
Some changes to fix background
AndrewSazonov Nov 16, 2020
b2da345
Rename instrument resolution vars
AndrewSazonov Nov 16, 2020
1869143
Add point names
wardsimon Nov 16, 2020
40ee09f
Point upper/lower
wardsimon Nov 16, 2020
e0943f7
Scale and x_offset implemented
wardsimon Nov 16, 2020
58c2cb8
Modify background label
AndrewSazonov Nov 17, 2020
cec38ed
Fix build script
AndrewSazonov Nov 17, 2020
8590fa6
Fixup build scripts
wardsimon Nov 17, 2020
0a98055
Merge remote-tracking branch 'origin/gsas' into gsas
wardsimon Nov 17, 2020
85e3c70
Update for specie work
wardsimon Nov 17, 2020
3ce84de
Recalculate sin(Th)/Lambda
AndrewSazonov Nov 17, 2020
8f07686
Set some experimental parameters
AndrewSazonov Nov 18, 2020
721d300
Fixup some serialization
wardsimon Nov 18, 2020
7f3b9ca
Keep temp.cif file for fitting process
AndrewSazonov Nov 19, 2020
44d6463
Fix sinTh/Lambda for CFML
AndrewSazonov Nov 19, 2020
c2108ed
Keep temp.cif for fitting with CFML
AndrewSazonov Nov 19, 2020
710aba3
Update to new CFML api
AndrewSazonov Nov 20, 2020
efb0372
Tidy up background work
wardsimon Nov 25, 2020
d47bfe9
More background tidying
wardsimon Nov 26, 2020
f12e168
Revert BG changes
wardsimon Nov 26, 2020
8713633
Debugging info for y_calc
AndrewSazonov Nov 26, 2020
77bff2e
Add fitting notebook
wardsimon Nov 27, 2020
e4474af
More fitting work
wardsimon Nov 27, 2020
40de2f0
Add CFML fitting notebook
AndrewSazonov Nov 27, 2020
13ec3f5
Update branches
wardsimon Dec 4, 2020
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50 changes: 50 additions & 0 deletions .devcontainer/Base.Dockerfile
Original file line number Diff line number Diff line change
@@ -0,0 +1,50 @@
# [Choice] Python version: 3, 3.9, 3.8, 3.7, 3.6
ARG VARIANT=3
FROM python:${VARIANT}

# [Option] Install zsh
ARG INSTALL_ZSH="true"
# [Option] Upgrade OS packages to their latest versions
ARG UPGRADE_PACKAGES="true"

# Install needed packages and setup non-root user. Use a separate RUN statement to add your own dependencies.
ARG USERNAME=vscode
ARG USER_UID=1000
ARG USER_GID=$USER_UID
COPY .devcontainer/library-scripts/common-debian.sh /tmp/library-scripts/
RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
# Remove imagemagick due to https://security-tracker.debian.org/tracker/CVE-2019-10131
&& apt-get purge -y imagemagick imagemagick-6-common \
# Install common packages, non-root user
&& bash /tmp/library-scripts/common-debian.sh "${INSTALL_ZSH}" "${USERNAME}" "${USER_UID}" "${USER_GID}" "${UPGRADE_PACKAGES}" \
&& apt-get autoremove -y && apt-get clean -y && rm -rf /var/lib/apt/lists/* /tmp/library-scripts

# Setup default python tools in a venv via pipx to avoid conflicts
ENV PIPX_HOME=/usr/local/py-utils \
PIPX_BIN_DIR=/usr/local/py-utils/bin
ENV PATH=${PATH}:${PIPX_BIN_DIR}
COPY .devcontainer/library-scripts/python-debian.sh /tmp/library-scripts/
RUN bash /tmp/library-scripts/python-debian.sh "none" "/usr/local" "${PIPX_HOME}" "${USERNAME}" "false" \
&& apt-get clean -y && rm -rf /tmp/library-scripts

# [Option] Install Node.js
ARG INSTALL_NODE="true"
ARG NODE_VERSION="none"
ENV NVM_DIR=/usr/local/share/nvm
ENV NVM_SYMLINK_CURRENT=true \
PATH=${NVM_DIR}/current/bin:${PATH}
COPY .devcontainer/library-scripts/node-debian.sh /tmp/library-scripts/
RUN if [ "$INSTALL_NODE" = "true" ]; then bash /tmp/library-scripts/node-debian.sh "${NVM_DIR}" "${NODE_VERSION}" "${USERNAME}"; fi \
&& apt-get clean -y && rm -rf /var/lib/apt/lists/* /tmp/library-scripts

# [Optional] If your pip requirements rarely change, uncomment this section to add them to the image.
# COPY requirements.txt /tmp/pip-tmp/
# RUN pip3 --disable-pip-version-check --no-cache-dir install -r /tmp/pip-tmp/requirements.txt \
# && rm -rf /tmp/pip-tmp

# [Optional] Uncomment this section to install additional OS packages.
# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
# && apt-get -y install --no-install-recommends <your-package-list-here>

# [Optional] Uncomment this line to install global node packages.
# RUN su vscode -c "source /usr/local/share/nvm/nvm.sh && npm install -g <your-package-here>" 2>&1
45 changes: 45 additions & 0 deletions .devcontainer/Dockerfile
Original file line number Diff line number Diff line change
@@ -0,0 +1,45 @@
{
"name": "Python 3",
"build": {
"dockerfile": "Dockerfile",
"context": "..",
"args": {
// Update 'VARIANT' to pick a Python version: 3, 3.6, 3.7, 3.8, 3.9
"VARIANT": "3",
// Options
"INSTALL_NODE": "true",
"NODE_VERSION": "lts/*"
}
},

// Set *default* container specific settings.json values on container create.
"settings": {
"terminal.integrated.shell.linux": "/bin/bash",
"python.pythonPath": "/usr/local/bin/python",
"python.linting.enabled": true,
"python.linting.pylintEnabled": true,
"python.formatting.autopep8Path": "/usr/local/py-utils/bin/autopep8",
"python.formatting.blackPath": "/usr/local/py-utils/bin/black",
"python.formatting.yapfPath": "/usr/local/py-utils/bin/yapf",
"python.linting.banditPath": "/usr/local/py-utils/bin/bandit",
"python.linting.flake8Path": "/usr/local/py-utils/bin/flake8",
"python.linting.mypyPath": "/usr/local/py-utils/bin/mypy",
"python.linting.pycodestylePath": "/usr/local/py-utils/bin/pycodestyle",
"python.linting.pydocstylePath": "/usr/local/py-utils/bin/pydocstyle",
"python.linting.pylintPath": "/usr/local/py-utils/bin/pylint"
},

// Add the IDs of extensions you want installed when the container is created.
"extensions": [
"ms-python.python"
]

// Use 'forwardPorts' to make a list of ports inside the container available locally.
// "forwardPorts": [],

// Use 'postCreateCommand' to run commands after the container is created.
// "postCreateCommand": "pip3 install --user -r requirements.txt",

// Uncomment to connect as a non-root user. See https://aka.ms/vscode-remote/containers/non-root.
// "remoteUser": "vscode"
}
45 changes: 45 additions & 0 deletions .devcontainer/devcontainer.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,45 @@
{
"name": "easyDiffractionLib dev",
"build": {
"dockerfile": "Dockerfile",
"context": "..",
"args": {
// Update 'VARIANT' to pick a Python version: 3, 3.6, 3.7, 3.8, 3.9
"VARIANT": "3.7",
// Options
"INSTALL_NODE": "true",
"NODE_VERSION": "lts/*"
}
},

// Set *default* container specific settings.json values on container create.
"settings": {
"terminal.integrated.shell.linux": "/bin/bash",
"python.pythonPath": "/usr/local/bin/python",
"python.linting.enabled": true,
"python.linting.pylintEnabled": true,
"python.formatting.autopep8Path": "/usr/local/py-utils/bin/autopep8",
"python.formatting.blackPath": "/usr/local/py-utils/bin/black",
"python.formatting.yapfPath": "/usr/local/py-utils/bin/yapf",
"python.linting.banditPath": "/usr/local/py-utils/bin/bandit",
"python.linting.flake8Path": "/usr/local/py-utils/bin/flake8",
"python.linting.mypyPath": "/usr/local/py-utils/bin/mypy",
"python.linting.pycodestylePath": "/usr/local/py-utils/bin/pycodestyle",
"python.linting.pydocstylePath": "/usr/local/py-utils/bin/pydocstyle",
"python.linting.pylintPath": "/usr/local/py-utils/bin/pylint"
},

// Add the IDs of extensions you want installed when the container is created.
"extensions": [
"ms-python.python"
]

// Use 'forwardPorts' to make a list of ports inside the container available locally.
// "forwardPorts": [],

// Use 'postCreateCommand' to run commands after the container is created.
// "postCreateCommand": "pip3 install --user -r requirements.txt",
"postCreateCommand": "curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python3 && export PATH=$PATH:$HOME/.poetry/bin",
// Uncomment to connect as a non-root user. See https://aka.ms/vscode-remote/containers/non-root.
// "remoteUser": "vscode"
}
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