Merge pull request #2 from hz-b/cleanup

Updated install instructions

.github/workflows/cmake-single-platform.yml

@@ -38,13 +38,13 @@ jobs:
 
  - name: install apt dependencies
  run: |
- sudo apt update
+ sudo apt-get update
  # gfortran ... currently for mad-ng gtpsa library
- sudo apt install g++ gfortran cmake make bison flex libarmadillo-dev
+ sudo apt-get install g++ gfortran cmake make bison flex libarmadillo-dev
  # deliberatly only installing a subset of boost
- sudo apt install libboost-chrono-dev libboost-thread-dev libboost-filesystem-dev libboost-program-options-dev libboost-regex-dev libboost-test-dev
- # for building the python interface ... hopefully python3-xarray is not needed this rather heavy
- sudo apt install pybind11-dev python3-pytest python3-pip python3-pybind11 # python3-xarray
+ sudo apt-get install libboost-chrono-dev libboost-thread-dev libboost-filesystem-dev libboost-program-options-dev libboost-regex-dev libboost-test-dev
+ # for building the python interface ... hopefully python3-xarray is not needed this is rather heavy
+ sudo apt-get install pybind11-dev python3-pytest python3-pip python3-pybind11
 
  - name: Configure cmake for gtpsa-cpp
  run: cmake gtpsa-cpp -B ${{github.workspace}}/gtpsa-cpp/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}
@@ -82,5 +82,14 @@ jobs:
  - name : thor-scsi-lib build and install python package
  run: gtpsa_PREFIX=/usr/local thor_scsi_PREFIX=/usr/local pip3 install -v ./python/
 
+ - name: install apt test dependencies
+ run: |
+ # xarray are heavy packages ... deliberatley only installed here
+ # as required for the tests
+ sudo apt-get install python3-pandas python3-scipy python3-xarray
+
  - name : thor-scsi-lib test python package
- run: pytest-3 python
+ # consider removing tests ....
+ # so more tests will be run
+ # bba_test needs scikit-learn ... don't want to blow that image
+ run: pytest-3 python/tests/

install.rst

@@ -10,6 +10,8 @@ python wrapper.
 Dependencies
 ------------
 
+- `gtpsa-cpp` provided by https://github.com/hz-b/gtpsa-cpp.git
+
 - modern c++ compiler C++17 or better
 
  - std::shared_ptr
@@ -26,6 +28,7 @@ Dependencies
 
  - flex and bison
 
+
 - modern python3
 
 Packages to be installed on Ubuntu 22 LTS
@@ -52,7 +55,7 @@ First clone the repository using
 
 .. code:: shell
 
- git clone https://github.com/jbengtsson/thor-scsi-lib.git
+ git clone https://github.com/hz-b/thor-scsi-lib.git
 
 
 change to the directory (persumably) `thor-scsi-lib`.
@@ -63,16 +66,14 @@ Then initialise submodules using the following command
 
  git submodule update --init
 
-*NB*: this command currently will pull a subrepository (`cmake4epics`).
-This repository currently does not support (llvm/clang). Thus build on
-MAC currently fails. A fix is currently worked on.
-
-
 
 Getting ready to build
 ----------------------
 
-create a directory "build"
+Please install first gtpsa-cpp. Have a look to the installation
+instructions provided there.
+
+Create a directory "build"
 
 .. code:: shell
 
@@ -144,20 +145,6 @@ python install procedure.
 Before you can use this script, you need to build the c++ library and install it
  to some path (called `/path/to/install/to` above).
 
-Directories with python modules
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Two python modules are provided
-
-* gtpsa: directory src/gtpsa/python
-* thor_scsi: directory python/
-
-Recommandation is to first build gtpsa and then thor scsi.
-The description below refers to both of them. Both directories are 
-refered to as `python` directory below.
-
-Installation instruction for one of the packages
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 The process of building the python package depends on the C++ headers and libraries.
 Thus it needs to know where these are installed. The process described below will

python/requirements.txt

@@ -1,2 +1,4 @@
 # Using PyBind11Extension
 pybind11>=2.6.0
+gtpsa
+pandas

python/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = thor_scsi
-version = 0.0.0
+version = 0.0.2
 url = https://github.com/jbengtson/thor-scsi-lib/
 author = Johan Bengtsson, Pierre Schnizer
 author_email = johan.bengtsson@helmholtz-berlin.de
@@ -23,6 +23,6 @@ requires = setup_tools
 
 [build_sphinx]
 project = 'thor_scsi'
-version = 0.0.0
-release = 0.0.0
+version = 0.0.2
+release = 0.0.2
 # source-dir = 'doc'

python/tests/knobbable_test.py

@@ -7,7 +7,7 @@
 from dataclasses import dataclass
 import numpy as np
 
-@pytest.mark.skip
+#@pytest.mark.skip
 def test_knob_quadrupole():
  length = 0.2
  K = 1.2
@@ -28,7 +28,6 @@ def test_knob_quadrupole():
  assert K_check == pytest.approx(K, rel=1e-12)
 
 
-@pytest.mark.skip
 def test_knob_horizontal_steerer():
  length = 0.0
  K = 0.1
@@ -51,7 +50,7 @@ def test_knob_horizontal_steerer():
  knobs.make_magnet_knobbable(nh_st, po=1, desc=desc, named_index=named_index)
 
 
-@pytest.mark.skip
+#@pytest.mark.skip
 def test_knob_vertical_steerer():
  length = 0.0
  K = 0.2
@@ -90,7 +89,6 @@ def analytic_x(*, K, length):
  return RMatrix(m11=m11, m12=m12, m21=m21, m22=m22)
 
 
-# @pytest.mark.skip
 def test_quadrupole_dependence_on_offset():
  """check that the parameter dependence on dx works as expected
 
@@ -136,12 +134,16 @@ def test_quadrupole_dependence_on_offset():
  {r_analytic.m21}, {r_analytic.m22}
  """
  print("analytic\n", txt)
+
+ for a_tpsa in [ps.x, ps.px]:
+ print(gtpsa.utils_df.tpsa2df(a_tpsa))
+
  # assert ps.x.get(dx=1) == pytest.approx(expected_dx_dependence, rel=1e-12)
  # fmt: on
  assert ps.x.get(x=1) == pytest.approx(r_analytic.m11, rel=1e-3)
- assert ps.x.get(dx=1) == pytest.approx(r_analytic.m12, rel=1e-3)
- assert ps.dx.get(x=1) == pytest.approx(r_analytic.m21, rel=1e-3)
- assert ps.dx.get(dx=1) == pytest.approx(r_analytic.m21, rel=1e-3)
+ assert ps.x.get(px=1) == pytest.approx(r_analytic.m12, rel=1e-2)
+ assert ps.px.get(x=1) == pytest.approx(r_analytic.m21, rel=1e-2)
+ assert ps.px.get(px=1) == pytest.approx(r_analytic.m22, rel=1e-2)
  # fmt: off
 
  # Estimate effect based on propagation
@@ -153,4 +155,3 @@ def test_quadrupole_dependence_on_offset():
  ps.set_zero()
  quad.propagate(calc_config, ps)
  print(ps.x, ps.px)
- assert False